SKRULLS READING ORDER: Infiltration (1995-2008)

Well, this one ended up being a lot longer than I'd expected, but I wanted to capture the key stuff from the first appearance of the Skrull Kill Krew right the way up to the SECRET INVASION: THE INFILTRATION tie-ins that lead up to SECRET INVASION. And I've certainly done that, but it's a beast!

Aside from the KREE-SKRULL WAR and the events of THE TRIAL OF REED RICHARDS (also covered in the previous Skrulls entries), most of the spotlighted stories below give you all the background reading you need to make the most sense of the entire SECRET INVASION event. If you just want the basics, just head on over to SECRET INVASION: THE INFILTRATION and go from there.

The Skrull Empire is now in disarray, but the X-Men discover a plot to infiltrate the Earth's super-human community and an alliance with Apocalypse. When all of that dies down, the Skrulls begin their full-scale invasion plans. And we had no idea they were infiltrating the Avengers and other super-teams, until it was too late!

I'll create a fourth entry at some point, but the last three reading order entries for these shape-shifting aliens will cover most of what you'd need to read before their biggest event, SECRET INVASION, will which no doubt influence the films at some point.

As always, I'd like to thank the guys over at the Marvel Chronology Project which I use as a basis and then work out my own version of the Marvel Universe continuity. Those guys have done all the heavy lifting for me.

MCG Notes:

• Issue listings in blue & black: The must-read Skrulls stories from this time period, along with any key related stories and often-forgotten tales that are worth a read.
• Issue listings in grey: Cameo appearances or stories of note that are non-essential or no longer considered 'required reading'.
• Chronology: Every appearance of the Skrulls from this period is included in chronological order - mapping out his timeline rather than just the order the issues were released.
• Spoilers: The issue/story overviews may include spoilers, so be warned!
• WANT TO KEEP IT SIMPLE? Scroll down to THE CORE LIST to see a version of this reading order without story descriptions, page-by-page breakdowns or less important appearances - just a list of the essentials.

See previous entries of the Skrulls reading order:

• 1962-1977: Rise of the Skrulls
• 1978-1994: Fall of the Skrulls

Skrull Kill Krew #1-5 (1995-1996) 
Humans learn they've gained shape-shifting powers from eating burgers made from the Skrulls that Mister Fantastic (Reed Richards) once turned into cows become the Skrull Kill Krew; their plan is to kill as many Skrulls as they can before they die!

Fantastic Four #393-395 (1994) 

Having grown close to the Human Torch (Johnny Storm) while she was posing as Alicia Masters, Lyja the Lazerfist tries to win him back by taking on the form of a human named 'Laura Green'. 

Blackwulf #7-10 (1994-1995) 

The Prime Skrull joined forces with Blackwulf and the Kree Starforce against the armies of Tantalus; Blackwulf kills Tantalus. 

Fantastic Four #396-397 (1995)

Fantastic Force #7 (1995)

Fantastic Four #400 (1995) 

Despite the Human Torch's open contempt for her, Lyja assists the Fantastic Four against Aron the Rogue Watcher during EVEN THE WATCHERS CAN DIE. 

Nova #15-16 (1995) 

First appearance of Muraitak - a Skrull member of the Nova Corps.

Silver Surfer #105 (1995) 

Empress S'Byll gets fired up when the Super-Skrull attacks the Silver Surfer without her authorisation. 

Fantastic Four: Atlantis Rising #1 (1995)

Fantastic Force #8-9 (1995)

Fantastic Four: Atlantis Rising #2 (1995) 

While dating the Human Torch as 'Laura Green', Lyja aids the Fantastic Force against Morgan le Fay and the Crimson Cadre in her true form; the Human Torch quits the Fantastic Four during ATLANTIS RISING. 

Force Works #13-14 (1995) 

First appearance of Hokk Algol - a Skrull whose intentions to force a Kree Starstealth team to be tried for war crimes brings him into conflict with Force Works. 

Force Works #15 (1995) 

First appearance of Kerth - Skrull slave of the extra-terrestrial Broker; Century frees Kerth from the Broker's control and promises to help him and the other slaves return to their home planets during DISTANT SONS.

Star Masters #1-3 (1995) 

First appearance of Morfex - a Skrull disguised as an Axi-Tun and a member of the Cosmic Commandos; when Morfex fails to apprehend Quasar, his true identity is revealed; Morfex ends up joining Quasar's Star Masters instead. 

Fantastic Four Unplugged #2 (1995) 

Lyja continues to ally herself with the FF, despite the Torch leaving.

Fantastic Four #403 (1995) 

Lyja the Lazerfist officially joins the Fantastic Four alongside the Invisible Woman, Thing and Ant-Man. 

Cosmic Powers Unlimited #4-5 (1996) 

Morfex and his fellow Star Masters defeat the Axi-Tun Lord Votan. 

Lunatik #2 (1996) 

First and only appearance of Lunatik's Skrull landlord, Rachman. 

Spider-Man Team-Up #2 (1996) 

The Silver Surfer and Spider-Man (Ben Reilly) get help from the Kralians of Kral IV while they hunt down Quasimodo and the Mad Thinker. 

Force Works #16 (1995) 

Kerth appears as Century stops the slaves from killing the Broker during DISTANT SONS / THE CROSSING. 

Century: Distant Sons #1 (1996) 

The Broker's former slaves eventually make an attempt on his life, but he kills many of them including Kerth during DISTANT SONS. 

Fantastic Four #404-407 (1995)

Fantastic Four Unplugged #3 (1996)

Fantastic Four Unlimited #12 (1995)

Fantastic Four #408-409 (1996) 

Lyja steps down as a member of the Fantastic Four when Mister Fantastic is revealed to be alive; the Human Torch returns to the team during STRANGE DAYS. 

Fantastic Four #410 (1996) 

Lyja continues dating the Human Torch as 'Laura Green', while the Thing starts to develop an interest in Lyja. 

Fantastic Four Unplugged #4 (1996)

Avengers Unplugged #3 (1996)
An eventful date with the Human Torch almost exposes 'Laura Green' as Lyja during DATE NITE! 

Europa #0 (1996) 

First and only appearance of the Skrulls of the Inquisition Crash - a group of Skrulls who crash-landed in Spain during the time of the Inquisition; the bodies of the Skrulls were eaten by a group of Inhumans the Inquisition had failed to kill, mutating them and passing their new abilities down to their offspring; the last of their generation are destroyed by SHIELD super-agent Gemini in the present day. 

Fantastic Four #411-412 (1996) 

Lyja continues to struggle with deceiving the Human Torch and is the only one who's aware that Namor allowed Mister Fantastic to defeat him in a fight over the Invisible Woman. 

Fantastic Four #414 (1996) 

The Thing finally figures 'Laura Green' is Lyja; Lyja tries to tell the Human Torch the truth, but he breaks off the conversation to deal with the threat of Hyperstorm during THE ROAD TO ONSLAUGHT. 

Fantastic Four #415-416 (1996) 

Lyja the Lazerfist reveals the truth about her 'Laura Green' persona to the Human Torch who, it turns out, knew who she was from the moment they first kissed; the Torch forgives Lyja while they fend off Onslaught's mental attacks during ONSLAUGHT.

Tales of the Marvel Universe #1 (1997) 

Lyja works through her grief following the death of the Fantastic Four in the final battle against Onslaught; she continues her life in the human form of 'Laura Green' during THE HAUNTING OF CASTLE DOOM. 

Captain America #3-7 (1998) 

First appearance of Sensational Hydra - a new, flamboyant Hydra leader who turns out to be a Skrull; the Skrull and his plan to cause disarray and mistrust across America is thwarted by Captain America. 

Deadpool #24 (1999) 

First and last appearance by Mrok whose plan to invade Earth is ended by Mithras - the 'cosmic messiah' that destroys him as it passes by.

X-Men #89 (1999) 

Uncanny X-Men #370 (1999) 

X-Men #90 (1999) 

Stranded in the past, the X-Men uncover a plot to replace Earth's heroes with Skrull Hero Imposters; the plan seemingly comes to an end when Galactus consumes the Skrull throneworld and the the X-Men return to the present during HISTORY REPEATS. 

Uncanny X-Men #371 (1999) 

X-Men #91 (1999)

First appearance of the Wolverine Imposter (though no clue is given at the time that he's really a Skrull) during RAGE AGAINST THE MACHINE. 

Contest of Champions II #1, 3-5 (1999)

'Wolverine' fights other heroes as part of the second 'Contest of Champions'.

Wolverine #140 (1999) 

'Wolverine' tests his disguise by interacting with Nightcrawler. 

X-Men Unlimited #24[1/2] (1999)

'Wolverine' fights the Silver Samurai.

Wolverine/The Punisher: Revelation #1-4 (1999)

'Wolverine ' teams up with the Punisher to stop a deadly mutant.

Wolverine #141-143 (1999) 

'Wolverine' tests his disguise by interacting with Alpha Flight and Jubilee.

Wolverine #144 (1999) 

Hulk #7-8 (1999)

'Wolverine' tests his fighting prowess by taking on the Hulk during GRUDGE MATCH.

Uncanny X-Men #372 (1999)

X-Men #92 (1999)

Gambit #8 (1999) 

Astonishing X-Men #1-3 (1999)

Professor X disbands the X-Men, forcing the various team members (including 'Wolverine') to go their separate ways; 'Wolverine' is killed by Death (the latest of the Horsemen of Apocalypse to take that name) during THE SHATTERING. 

Uncanny X-Men #375 (1999)

X-Men #95 (1999)

Wolverine #145 (1999) 

First appearance of Granok (a Skrull scientist) and the band of outcast mutant Skrulls who will become Cadre K; Professor X reveals the deceased 'Wolverine' is actually a Skrull (the Wolverine Imposter was killed by 'Death' - the real Wolverine); Granok is revealed to be behind the experiments on mutant Skrulls and the one who gave the Wolverine Imposter his healing abilities during THE SHATTERING.

Uncanny X-Men #376 (2000)

X-Men #96 (2000)

Uncanny X-Men #377 (2000)

X-Men #97 (2000) 

The band of outcast mutant Skrulls side with the X-Men against Apocalypse and his Skrull allies during APOCALYPSE: THE TWELVE.

Uncanny X-Men #378 (2000)

 X-Men #98 (2000) 

The mutant Skrulls continue to assist the X-Men while Apocalypse warps reality around them during AGES OF APOCALYPSE. 

Uncanny X-Men #379 (2000) 

Professor X leaves the X-Men in favour of training the mutant Skrulls how to use their powers and helping them free other downtrodden members of their race in space during MUTANTS NO MORE.

Captain Marvel #8-10 (2000) 
Intelligentsia (the Skrull version of the Supreme Intelligence) orders the Super-Skrull to head to Earth and take out Marlo Chandler-Jones when she gains reality-warping powers. 

Avataars #1-3 (2000) 

The Shaper of Worlds is among the god-like beings who create an alternate Earth for their own amusement. 

Maximum Security: Dangerous Planet #1 (2000) 

Skrull ambassador Kreddick pleads with the Intergalactic Council to deal with the interfering Earthlings who are always sticking their noses into everyone else's affairs during MAXIMUM SECURITY.

Uncanny X-Men #387 (2000)

Bishop #15 (2000)

X-Men #107 (2000)

Thunderbolts #45 (2000)

Maximum Security #2 (2000)

X-Men Unlimited #29 (2000)

Maximum Security #3 (2001)

Professor X's band of mutant Skrulls - now known as Cadre K - defend the universe from Ego the Living Planet, which somehow only ends up making things worse; Professor X leads Cadre K against the Intergalactic Council when they decide to turn Earth into a prison for cosmic criminals; Moonstone of the Thunderbolts learns of the existence of the Chosen Eight of Fate - a group of warriors from eight different alien races (including a Skrull) genetically engineered to protect the universe (also known as the Guardians of the Galaxy); Cadre K assist in destroying the barrier that keeps humanity on Earth and holds all the alien criminals in during MAXIMUM SECURITY. 

Thunderbolts #46 (2001) 

Moonstone learns the origin of the Chosen Eight of Fate.

Fantastic Four #37 (2001) 

A group of Skulls are sent to assassinate the Super-Skrull for his association with the old regime as a new Skrull Empire begins to rebuild; the Super-Skrull escapes and remains on Earth disguised as a special effects specialist in Hollywood. 

Thing: Freakshow #1-4 (2002) 

Paibok the Power Skrull returns, this time with a power upgrade that's left him looking worse for wear; his efforts to capture a young Watcher lead him into trouble with the Thing and the Kree. 

Craptacular B-Sides #1-3 (2002-2003) 

The B-Sides discover a town called Raven's Perch, populated by Skrulls who are living quite happily as 'humans'. 

New Avengers #40 (20098)
Veranke is brought out of exile by a faction of Skrulls who begin a plot to infiltrate the superhuman community of planet Earth by replacing them with super-powered Skrull imposters; Veranke opts to replace Spider-Woman (Jessica Drew); do not read this until SECRET INVASION.

New Avengers #42(pp.3-7, 14-15) (2008)
Under orders form Nick Fury, Jessica Drew agrees to let Hydra give her back her powers and work as a double-agent for them and SHIELD; the Hydra agents are really Skrulls and Jessica is replaced; Queen Veranke becomes 'Jessica Drew' and gains her powers; do not read until SECRET INVASION.

Marvel Team-Up #2-6 (2005) 

First appearance of Titannus - a Skrull born without shape-shifting abilities who became part of the Super-Skrull program, gaining enhanced strength and healing; Titannus is exiled and arrives on Earth, looking for trouble.

Young Avengers #1-6 (2005) 

First appearance of Hulkling, a member of the Young Avengers (who's initially unaware of his true origins).

Mighty Avengers #12(pp.1-17) (2008)
On the run from SHIELD, Nick Fury faces an assassination attempt by a Skrull disguised as Contessa Valentina Allegra de la Fontaine; do not read until SECRET INVASION.

New Avengers #1-3(pp.1-21) (2005)
A mystery benefactor (aka 'Elektra', aka a Skrull imposter) employs Electro to cause a breakout at the Raft prison for super-criminals; as 'Jessica Drew', Queen Veranke fights alongside Captain America, Iron Man, Spider-Man, Luke Cage and others in an effort to stop the breakout (though Veranke's identity is not revealed until much later) during BREAKOUT.

Mighty Avengers #15(pp.17-18) (2008)
New Avengers #42(p.15) (2008)
Criti Noll replaces Hank Pym and is given Pym's powers by Veranke; Veranke as 'Jessica Drew' discusses Captain America's offer of Avengers membership 'Hank Pym'; do not read until SECRET INVASION.

New Avengers #3(pp.22)-4(pp.1-7) (2005)
After checking in with Hydra, 'Jessia Crew' joins the new Avengers as 'Spider-Woman' during BREAKOUT.

New Avengers #42(p.17-18) (2008)
The Avengers reveal to 'Spider-Woman' that the Scarlet Witch went mad and is now with Magneto; do not read until SECRET INVASION.

New Avengers #4(pp.19-22)-6 (2005)
The Avengers discover a conspiracy with SHIELD in the Savage Land during BREAKOUT.

Marvel Team-Up #7-13 (2005) 

Titannus attacks Japan, clashing with Sunfire; he's defeated by Wolverine, Spider-Man, Doctor Strange, Hulk, Ms Marvel, Nova and She-Hulk; Titannus commits suicide when he's rejected by his ex-girlfriend. 

Marvel Team-Up #20 (2006) 

First appearance of the Curtis Doyle's neighbour; Titannus is revealed to have survived and regrown his own head.

New Avengers #7-10 (2005)
Alongside the new Avengers, 'Spider-Woman' helps the Sentry overcome the Void, regain his senses and join the team.

Hercules #4 (2005)
'Spider-Woman' is present when Hercules steals Captain America's shield as one of his twelve labours.

Young Avengers #8 (2005)

Young Avengers Special #1 (2006) 

Hulkling reveals how he learned about his powers and joined the Young Avengers during SECRET IDENTITIES.

Young Avengers #9-12 (2005-2006) 

Hulkling learns he's the half-Kree, half-Skrull son of Captain Marvel (Mar-Vell) and Princess Anelle; both the Skrulls (led by the Super-Skrull) and the Kree try to claim him, but he's defended by the Avengers (including Veranke as 'Spider-Woman') and his fellow Young Avengers.

Amazing Spider-Man #519-520, 522-523 (2005)
'Spider-Woman' is among the members of the Avengers helping Spider-Man adjust to being part of a team.

Runaways #7-8 (2005) 

First appearance of Xavin, a young Super-Skrull who was due to marry Karolina Dean to end the Skrull-Majesdane War; to end the bloodshed, Karolina leaves Earth with Xavin.

Marvel Knights: Spider-Man #13-18 (2005) 

A new super-hero, Virtue (Ethan Edwards), learns he's actually a Skrull thanks to Spider-Man. 

Drax the Destroyer #1-4 (2005-2006) 

Paibok the Power Skrull returns, all back to his old self; he avoids incarceration when the prison ship he's on crashlands on Earth; he kills Drax the Destroyer who somehow comes back from the dead, looking for revenge; Paibok surrenders himself to the cosmic authorities to avoid facing Drax during ANNIHILATION.

New Avengers #42(pp.19-22) (2008)
New Avengers #45(pp.1-6) (2008)
Maria Hill questions 'Spider-Woman', believing her to be a Hydra agent; 'Spider-Woman' gives 'Yellowjacket' the order to kill the Scarlet Witch, then reality shifts and she finds herself in an altered universe where Magneto rules and she's a member of SHIELD; do not read until SECRET INVASION.

House of M #2 (2005)
'Jessica Drew' keeps her cover, functioning as an agent of SHIELD during HOUSE OF M.

New Avengers #45(pp.7-12) (2008)
Skrull 'Hank Pym' struggles to keep his sanity in the new reality; Veranke predicts a war against the mutants; so not read until SECRET INVASION. 

House of M #3 (2005)

Pulse #10 (2005)

House of M #6-7 (2005)
'Jessica Drew' pretends to allow her memories to be restored and sides with the Avengers against Magneto during HOUSE OF M.

New Avengers #45(pp.13-19) (2008)
'Jessica Drew' witnesses the climactic confrontation with Magneto, the death of Hawkeye and the restoration of reality; do not read until SECRET INVASION.

House of M #8 (2005)

'Spider-Woman' cameo; 'Spider-Woman' alludes to not being fully aware of what just happened to reality during HOUSE OF M.

Uncanny X-Men #466 (2006) 

The WarSkrull called Flaw and his fellow Shi'ar Death Commandos wipe out the Grey family to end the bloodline and prevent the birth of another Phoenix host; only the time-displaced Marvel Girl (Rachel Grey) survives during DECIMATION. 

Runaways #9, 12 (2005-2006)
'Spider-Woman' meets the Runaways (without Xavin as a member).

New Avengers #11-15 (2005-2006)
Captain America becomes suspicious when he realises 'Spider-Woman' sees to have an agenda of her own, outside of being one of the Avengers.

New Thunderbolts #12 (2005)
A very naked 'Spider-Woman' pours drinks for the Purple Man (Zebediah Killgrave) while under his control; she's freed by the Thunderbolts.

Marvel Team-Up #15 (2006)
'Spider-Woman' cameo; the Avengers meet Invincible.

Civil War: Choosing Sides #1[6/6] (2006)
'Spider-Woman' cameo.

She-Hulk #1 (2005)
'Spider-Woman' cameo; Captain America and 'Spider-Woman' check in with She-Hulk.

She-Hulk #3 (2006) 

First appearance of General Kravo; Kravo's plot to overthrow the Djaigon throne is smashed by She-Hulk.

Ms Marvel #1 (2006)
Carol Danvers catches up with her friend, 'Jessica Drew', during BEST OF THE BEST.

Sentry #1-2 (2005)
'Spider-Woman' cameos; the Sentry fights alongside the New Avengers.

Doc Samson #1 (2006) 

Doc Samson's patient is a Skrull receiving counselling after he tried to nuke planet Earth. 

Wolverine #36-37 (2006)
'Spider-Woman' and the other Avengers go after Wolverine when he appears to go rogue during DECIMATION / ORIGINS & ENDINGS.

Uncanny X-Men #469-471 (2006) 

Marvel Girl and the X-Men hunt down Flaw and his fellow Death Commandos. 

The Pulse #12-13 (2006)
'Spider-Woman' and the other Avengers are on-hand when Jessica Jones gives birth during HAPPILY EVER AFTER.

Marvel Holiday Special #1[2/3] (2005)
Iron Man and Yellowjacket prank 'Spider-Woman' with a device that constantly puts her under the mistletoe; 'Spider-Woman' kisses Iron Man, Captain America and almost kisses Wolverine before she realises what they're up to.

New Thunderbolts #13-14 (2005-2006)
The Commission on Superhuman Activities hire the Thunderbolts to give the Avengers a humiliating defeat, which they do; 'Spider-Woman' clashes with Joystick; during RIGHT OF POWER.

Friendly-Neighborhood Spider-Man #2-3 (2006)
Marvel Knights Spider-Man #21 (2006)
Amazing Spider-Man #527 (2006)
Friendly-Neighborhood Spider-Man #4 (2006)
Marvel Knights Spider-Man #22 (2006)
'Spider-Woman' is among the Avengers who witness the death and rebirth of Spider-Man during THE OTHER: EVOLVE OR DIE.

Mighty Avengers #14(pp.10-12) (2008)
'Spider-Woman' and her team of Skrull infiltrators discuss how to take down the Sentry; do not read until SECRET INVASION.

Black Panther #16 (2006)
'Spider-Woman' cameo.

Runaways #17-18 (2006) 

Xavin and Karolina Dean return to Earth after wedding ceremony goes seriously wrong; having narrowly escaped with their lives, they rejoin the Runaways.

New Avengers #17-20 (2006) 

'Spider-Woman' and her fellow Avengers battle the Collective (a man who houses all of the expelled mutant powers); Hulking makes a cameo appearance during DECIMATION. 

New Avengers Annual #1 (2006)
'Spider-Woman' attends Luke Cage and Jessica Jones' wedding during HAPPILY EVER AFTER.

Marvel Team-Up #21-25 (2006) 

When Curtis Doyle becomes the costumed Freedom Ring, his neighbour reveals himself to be the new hero known as Crusader and becomes his mentor; Freedom Ring dies in battle against the resurrected Titannus; Crusader adopts the ring that gave Freedom Ring his powers and uses it to defeat Titannus.

Thing #8 (2006)
'Spider-Woman' is among the costumed adventurers taking part in the Thing's Super Hero Poker Tournament.

Runaways #19-21 (2006) 

Xavin and the Runaways face the other-dimensional Gibborim. 

Annihilation Prologue #1 (2006) 

While the Super-Skrull spies on the Kree, he learns of the destruction of two Skrull systems by the Annihilation Wave during ANNIHILATION. 

Iron Man #7-8, 10-12 (2006)
Iron Man appears to go rogue, bringing him into conflict with the Avengers (including 'Spider-Woman').

New Avengers #45(pp.20-23) (2008)

The undercover Skrulls plot their next move, now that the mutant population of Earth is greatly diminished; Veranke reveals that two Skrull systems have been destroyed by the Annihilation Wave, fueling the infiltrators' will to succeed in their mission; do not read until SECRET INVASION.

Civil War #1 (2006)
Wolverine #42 (2006) 

Hulkling and 'Spider-Woman' are among the gathered heroes following the destruction of Stamford during CIVIL WAR.

Annihilation: Super-Skrull #1 (2006) 

First appearance of R'Kin and Princess S'Bak; the Super-Skrull disobeys Princess S'Bak's orders and takes on the Harvester of Sorrows himself in an effort to save his son's home planet ANNIHILATION. 

Marvel Holiday Spectacular #1[3/14] (2009)
A Skrull replaces a regular civilian named Patrick and celebrates Christmas with the man's family.

Annihilation: Super-Skrull #2 (2006)
The Super-Skrull and his biggest fan, R'Kin, head into the Negative Zone during ANNIHILATION.

Civil War #2 (2006) 
Hulkling and his fellow Young Avengers are rescued by the registered heroes led by Captain America during CIVIL WAR.

Annihilation: Super-Skrull #3-4 (2006) 
Super-Skrull kills R'Kin for betraying him and destroys the Harvester of Sorrows but is too late to save his son or himself from death during ANNIHILATION. 

Civil War: Young Avengers & Runaways #1-4 (2006) 
Hulkling and the Young Avengers meets Xavin and his fellow Runaways when they clash with the interdimensional Kree warrior Marvel Boy during CIVIL WAR. 

New Avengers #23 (2006)
Realising Hydra and SHIELD no longer trust her, 'Spider-Woman' joins Captain America's Secret Avengers because she has nowhere else to go during CIVIL WAR. 

Runaways #22-24 (2007) 
Xavin and the Runaways face the Gibborim and are almost arrested by Iron Man. 

Annihilation: Ronan #2-4 (2006) 
Talos the Untamed comes close to being consumed by the Annihilation Wave during ANNIHILATION. 

Cable & Deadpool #30 (2006) 
Hulkling battles Deadpool during CIVIL WAR. 

Uncanny X-Men #478 (2006) 
A team of space-faring X-Men led by Havok discover a group of Warskrulls.

Civil War #5 (2006)
Punisher War Journal #2(p.10) (2007)
Civil War #6(pp.6-9) (2007)
Punisher War Journal #2(p.22) (2007)
Black Panther #25(p.4) (2007)
Civil War #6(pp.16-22)-7(pp.1-7) (2007)
As members of the Secret Avengers, Hulkling and 'Spider-Woman' break into Prison 42 to free the captured heroes during CIVIL WAR.

Civil War: The Return #1[1/2] (2007)
First appearance of 'Captain Marvel' (Khn'nr); 'Captain Marvel' is revealed to be the warden of Prison 42 in the Negative Zone, apparently having been pulled from the past before his death during CIVIL WAR.

Amazing Spider-Man #538 (2007)
Black Panther #25(pp.7-20) (2007)
Civil War #7(pp.17-24) (2007)
Captain America's Secret Avengers lose the Civil War; 'Spider-Woman' aligns with Luke Cage's new Secret Avengers, opposing Superhuman Registration during CIVIL WAR.

Secret Invasion Prologue #1 (2007)
Dum Dum Dugan is replaced with a Skrull imposter; do not read until SECRET INVASION.

Civil War: The Initiative #1 (2007)
Ms Marvel (Carol Danvers) tries to recruit 'Spider-Woman' back into Iron Man's registered Avengers; 'Spider-Woman' turns her back on Ms Marvel but learns Captain America is alive during CIVIL WAR / THE INITIATIVE / THE ULTRON INITIATIVE / REVOLUTION.

New Avengers #28(pp.5-19)-29(pp.4-13) (2007)
The Secret Avengers (including 'Spider-Woman') are lured into a trap when they investigate the rumour that Captain America is alive; Iron Man's Mighty Avengers fail to capture the Secret Avengers during THE INITIATIVE / REVOLUTION.

Fallen Son: The Death of Captain America - Avengers #1 (2007)
Fallen Son: The Death of Captain America - Iron Man #1 (2007)
'Spider-Woman' discusses the state of the nation following the death of Captain America with her fellow Secret Avengers during FALLEN SON: THE DEATH OF CAPTAIN AMERICA.

Captain America #26 (2007)
'Spider-Woman' cameo; the Secret Avengers watch coverage of Tony Stark's speech at Captain America's funeral during THE INITIATIVE / FALLEN SON: THE DEATH OF CAPTAIN AMERICA.

Mighty Avengers #17 (2008)
'Spider-Woman' deals with the rogue 'Hank Pym' Skrull; do not read until SECRET INVASION.

New Avengers #29(pp.18-21) (2007)
The New Avengers learn Echo is in trouble and head to Japan to avoid capture during THE INITIATIVE / REVOLUTION.

New Avengers #27-28(pp.1-4, 20-22), 29(pp.1-3, 22)-30 (2007)
The Secret Avengers head to Japan and battle the Hand to rescue Echo during REVOLUTION / THE INITIATIVE.

New Avengers #31 (2007)
Echo kills 'Elektra', revealing her to be a Skrull imposter during REVOLUTION / THE INITIATIVE / SECRET INVASION: THE INFILTRATION.

New Avengers #32 (2007)
The Secret Avengers take the Skrull Elektra corpse back to America with them and wonder who else among them might be a Skrull; an EMP (caused by Ultron) hits the team's jet, knocking it out of the sky; 'Spider-Woman' renders Wolverine unconscious and takes the 'Elektra' corpse during THE TRUST / THE ULTRON INITIATIVE / SECRET INVASION: THE INFILTRATION.

Mighty Avengers #15(p.10) (2008)
The infiltrating Skrulls discover how to penetrate Stark technology; 'Hank Pym' advises 'Jessica Drew' to summon the armada; do not read until SECRET INVASION.

Mighty Avengers #6 (2008)
After the Mighty Avengers defeat Ultron, Iron Man is visited by 'Spider-Woman' who brings him the corpse of the 'Elektra' Skrull during THE INITIATIVE / THE ULTRON INITIATIVE.

Mighty Avengers #7 (2008)
'Spider-Woman' reveals to Iron Man that the Secret Avengers believe he's a Skrull'; Iron Man and 'Spider-Woman' agree to keep the 'Elektra' Skrull a secret between them and she agrees to join the Mighty Avengers during SECRET INVASION: THE INFILTRATION / VENOM BOMB.

Mighty Avengers #8(pp.1-19) (2008)
New Avengers #36 (2008)
Mighty Avengers #8(pp.21-22)-9, 11 (2008)
'Spider-Woman' and the other Mighty Avengers fight alongside her former Secret Avengers team mates against Symbiote-infected New Yorkers when Doctor Doom appears to launch an attack on the US; the Secret Avengers learn 'Spider-Woman' has switched sides; Wolverine breaks into Avengers Tower and aggressively questions 'Spider-Woman' over her betrayal until he's interrupted by the Black Widow; 'Spider-Woman' and her fellow Mighty Avengers apprehend Doctor Doom in Latveria during VENOM BOMB.

Annihilation Saga #1 (2006)
Annihilation #2-3, 5 (2006-2007)
Annihilation: Heralds of Galactus #1[1/2] (2007)
Talos the Untamed fights alongside the forces opposing Annihilus; Paibok the Power Skrull is forced to side withs Ravenous and Annihilus when he's mind-controlled by Negative Zone bugs; the Super-Skrull is mysteriously resurrected and fights against the Annihilation Wave; the Super-Skrull opposes the rulers of the Kree when he finds himself allied with Ronan the Accuser; Paibok the Power Skrull is left to die in space by Terrax during ANNIHILATION.

Black Panther #31-34 (2007) 
The new Fantastic Four find themselves stranded on the Skrull world Kral IV, surrounded by the gangster-themed Kralians of Kral during FOUR THE HARD WAY.

New Warriors #2 (2007)

'Spider-Woman' cameo during THE INITIATIVE.

Wisdom #1-6 (2007) 

First appearance of John the Skrull, an agent of MI13 who permanently emulates 'John Lennon'.

Avengers: The Initiative #4(pp.11-13) (2007)

World War Hulk #2(pp.1-13) (2007)

Avengers: The Initiative #4(pp.18-22) (2007)

World War Hulk #2(pp.29-35), 4-5 (2007-2008)

'Spider-Woman' is among the heroes defeated by the Hulk when he returns to Earth during WORLD WAR HULK.

She-Hulk #21 (2007) 

Hulkling is revealed to have been impersonated by the Hulkling of Earth-721 who recently spent some time with the 50 State Initiative.

Avengers: The Initiative Annual #1 (2008)

The Revolutionary of the Liberteens reports back to his Skrull masters, revealing there's a Skrull on every team in the 50-State Initiative during SECRET INVASION: THE INFILTRATION.

Avengers: The Initiative #8-10, 12 (2008) 

Crusader joins the Initiative in the hope of being accepted as a fully-fledged superhero while keeping his Skrull origins to himself.

Breaking into Comics The Marvel Way #1[6/6] (2010)

'Spider-Woman' and Iron Fist flirt while taking down the Hate-Monger.

Marvel Holiday Special #1[3/4] (2007)

First appearance of 'Irving Griffin'; a Skrull replaces Daily Bugle editor Irving Griffin when staff journalist Lester pursues a story about the Skrulls. 

X-Men: Emperor Vulcan #1, 3 (2007-2008) 

Flaw and his fellow Death Commandos fight on behalf of the violent new Shi'ar emperor Vulcan.

Cable & Deadpool #50 (2008)

'Spider-Woman' cameo.

She-Hulk #22-24 (2007-2008) 

First appearance of Jazinda; She-Hulk is joined in her new role as a bail enforcement agent with a new partner, Jazinda, who turns out to be a Skrull on the run from her own people.

New Avengers #38-39 (2008)

Fearing for her child's safety, Jessica Jones leaves the Secret Avengers in favour of the relative safety of Avengers Tower (current residence of 'Spider-Woman'); a Skrull tries and fails to replace Echo during SECRET INVASION: THE INFILTRATION.

She-Hulk #25-27 (2007-2008) 

Jazinda is forced to kills a murderous alien.

Captain Marvel #1-3(pp.1-12) (2008) 

Iron Man locates 'Captain Marvel' in Paris and brings him back to America where he makes a very public return fighting the 'Cobalt Man'; 'Captain Marvel' is pursued by 'Kree soldiers' who are secretly Skrulls during SECRET INVASION: THE INFILTRATION. 

Annihilation: Conquest - Wraith #2-4 (2007-2008)

Annihilation: Conquest #1-4, 6 (2008)

The Super-Skrull becomes a Phalanx slave and is tasked with bringing down the Kree Wraith; Wraith frees the Super-Skrull from Phalanx control and the two become allies; Wraith, Ronan and the Super-Skrull help bring about an end to the Phalanx control of Kree space during ANNIHILATION: CONQUEST.

Ms Marvel #24 (2008)

Iron Man breaks his silence when he informs SHIELD unit Operation: Lightning Storm that their leader, Ms Marvel, is a Skrull impersonator.

Ms Marvel #25-27(pp.1-16) (2008)

First appearances of Rl'nnd and 'Ms Marvel'; Machine Man and Sleepwalker of Operation: Lightning Storm pursue the real Ms Marvel instead of the Skrull 'Ms Marvel'; the real Ms Marvel kills the new Super-Skrull, Rl'nnd; the captured Skrull 'Ms Marvel' utters the words "he loves you" when she blows herself up, destroying Lightning Storm's Mini-Carrier during SECRET INVASION: THE INFILTRATION.

Young Avengers Presents #2 (2008) 

Hulkling meets his father, 'Captain Marvel' (not realising he's a Skrull who believes himself to be the real Captain Marvel) during SECRET INVASION: THE INFILTRATION.

Captain Marvel #3(pp.13-22)-5 (2008) 

The religious cult called the Brotherhood of Hala (inspired by Captain Marvel's apparent resurrection), is revealed to be infested with Skrulls; 'Captain Marvel' learns he's actually a Skrull called Khn'nr; Khn'nr decides to betray the Skrulls and abort his true mission inspired by the spirit of the real Captain Marvel during SECRET INVASION: THE INFILTRATION.

She-Hulk #28-30 (2008) 

Jazinda and She-Hulk's bounty hunting activities lead them into a brawl with Hercules. 

Fantastic Four #556-557 (2008) 

Hulkling and 'Spider-Woman' cameos.

Young Avengers Presents #3 (2008) 

Hulkling convinces his boyfriend, Wiccan, to seek out the Scarlet Witch.

FF #562 (2008)
'Spider-Woman' cameo.

Avengers/Invaders #2-3, 7-12 (2008-2009)
'Spider-Woman' and the Mighty Avengers are reunited with the Secret Avengers when the Invaders arrive in the present day.

Hulk #8[2/2]-9[2/2] (2009)

'Spider-Woman' joins the Lady Liberators, assisting She-Hulk against Red Hulk during THE REVENGE OF THE LADY LIBERATORS.

Runaways #25-30 (2007-2008) 

Xavin and the Runaways are temporarily stranded in the past.

New Avengers: Illuminati #5 (2008) 

Iron Man takes the body of the 'Elektra' imposter to the Illuminati, only to discover 'Black Bolt' is also a Skrull during SECRET INVASION: THE INFILTRATION.

Ms Marvel #27(pp.17-22) (2008)

The Skrulls began their full-scale invasion of Earth during SECRET INVASION: THE INFILTRATION.

A version of this reading order without story descriptions, page-by-page breakdowns or less important appearances:

• Skrull Kill Krew #1-5
• Silver Surfer #105
• Spider-Man Team-Up #2
• Captain America #3-7
• X-Men #89
• Uncanny X-Men #370
• X-Men #90
• Hulk #8
• Astonishing X-Men #1-3
• Uncanny X-Men #375
• X-Men #95
• Wolverine #145
• Captain Marvel #8-10
• Fantastic Four #37
• Young Avengers #1-6
• Young Avengers Special #1
• Young AVengers #9-12
• Runaways #7-8
• Runaways #17-18
• Annihilation Prologue #1
• Annihilation: Super-Skrull #1-4
• New Avengers #28-32
• Mighty Avengers #6-7
• Annihilation #2-3, 5
• Avengers: The Initiative Annual #21
• New Avengers #38-39
• Captain Marvel #1-3
• Annihilation: Conquest #1-6
• Ms Marvel #24-27
• Young Avengers Presents #2
• Captain Marvel #4-5
• New Avengers: Illuminati #1, 5
• Secret Invasion Prologue #1

The Skrulls reading order will conclude:

• 2008-2015: Invasion!

Skrull Kill Krew
Skrulls Must Die! - The Complete Skrull Kill Krew
Both include...

Skrull Kill Krew #1-5

Fantastic Four Epic Collection vol.25: Strange Days
Includes...

Fantastic Four #403, 415-416

Tales of the Marvel Universe #1

Captain America by Waid & Garney Omnibus
Captain America: To Serve and Protect
Include ...

Captain America #3-7

X-Men: The Magneto War
Includes...

Uncanny X-Men #370

X-Men #89-90

Hulk by Byrne & Garney
Includes...

Hulk #7-8

Wolverine Epic Collection vol.12: Shadow of Apocalypse
Includes...

Hulk #8

Wolverine #144-145

X-Men: The Shattering
Includes...

 Astonishing X-Men #1-3

Uncanny X-Men #372, 375

X-Men #92, 95

X-Men vs Apocalypse: The Twelve Omnibus 
Includes...

Astonishing X-Men #1-3

Uncanny X-Men #372, 376-378

Wolverine #145

X-Men #92, 95-98

Fantastic Four: Flesh and Stone
Includes...

Fantastic Four #37

Young Avengers vol.1: Sidekicks
Young Avengers #1-6

Young Avengers vol.2: Family Matters
Young Avengers #7-12

Young Avengers Special #1

Young Avengers HC
Young Avengers by Heinberg & Cheung - The Complete Collection
Young Avengers Ultimate Collection
All include...

Young Avengers #1-12

Young Avengers Special #1

Runaways vol.2: Teenage Wasteland HC
Runaways vol.5: Escape to New York
Include...

Runaways #7-8

Runaways vol.3: The Good Die Young HC
Runaways vol.6: Parental Guidance
Both include...

Runaways #17-18

Runaways Omnibus
Runaways - The Complete Collection vol.2
Both include...
Runaways #7-8, 17-18

Annihilation Omnibus
Includes...

Annihilation #2-3, 5

Annihilation: Heralds of Galactus #1

Annihilation Prologue #1

Annihilation Saga #1

Annihilation: Super-Skrull #1-4

Annihilation - The Complete Collection vol.1
Includes...

Annihilation Prologue #1

Annihilation: Super-Skrull #1-4

New Avengers vol.3 HC
Includes...

Civil War: The Initiative #1

New Avengers #23, 27-31

Captain Marvel: Secret Invasion
Civil War: Front Line HC
Secret Invasion: Captain Marvel
Include...

Civil War: The Return #1

Secret Invasion
Secret Invasion by Brian Michael Bendis Omnibus
Include...

Mighty Avengers #7

New Avengers #31-32, 39

New Avengers: Illuminati #5

Secret Invasion Prologue #1

New Avengers by Brian Michael Bendis - The Complete Collection vol.3
Includes Civil War: The Initiative #1, New Avengers #28-32, 36 and New Avengers: The Illuminati #5

New Avengers vol.6: Revolution
Includes...

New Avengers #27-31

New Avengers vol.4 HC
Includes...

New Avengers #32, 36

New Avengers: The Illuminati #5

New Avengers vol.7: The Trust
Includes...

New Avengers #32, 36

Mighty Avengers vol.1: The Ultron Initiative
Includes...

Mighty Avengers #6

Mighty Avengers vol.2: Venom Bomb
Includes...

Mighty Avengers #7-9, 11

Mighty Avengers Assemble! HC
Mighty Avengers by Brian Michael Bendis - The Complete Collection
Includes...

Mighty Avengers #6-9, 11

Secret Invasion: The Infiltration
Includes...

Avengers: The Initiative Annual #1

Mighty Avengers #7

New Avengers #31-32, 38-39

New Avengers: Illuminati #5

New Avengers vol.5 HC
New Avengers vol.8: Secret Invasion, Book 1
New Avengers by Brian Michael Bendis - The Complete Collection vol.4
All include...

New Avengers #38-39

Annihilation: Conquest vol.2
Annihilation: Conquest Omnibus
Both include... 

Annihilation: Conquest #1-4, 6

Annihilation: Conquest - Wraith #2-4

Captain Marvel: Carol Danvers - The Ms Marvel Years vol.2
Includes...

Ms Marvel #24-27

Secret Invasion: Rise of the Skrulls
Includes...

Avengers: The Initiative Annual #1

Captain Marvel #1-5

Ms Marvel #25-27

Ms Marvel vol.5: Secret Invasion
Includes...

Ms Marvel #25-27

Young Avengers Presents
Includes...

Young Avengers Presents #2

New Avengers: Illuminati
Includes...

New Avengers: Illuminati #1, 5