Secret Invasion #1

S.W.O.R.D. is the acronym for Sentient World Observation and Response Department, the planet’s counter-terrorism and intelligence agency which deals with extraterrestrial threats.

Stark systems could not stop or inoculate the software virus but detected it as “alien”, which is strange. If you think about it, “alien” code will just not run in “local” computer systems, making infection impossible.

Mr Fantastic must fake surprise when Iron Man shows him the body of Skrull-Elektra because he's already been shown it in Illuminati #5. Henry Pym must fake surprise because *he's* a Skrull.

The New Avengers arrive at Avengers Tower via Cloak's cloak, to steal the quinjet. Dr Strange isn't with the NAv because he's recovering from World War Hulk. Wasp isn't shown with the Mighty Av this issue but she must just be too small to see because she's here next ish.

The place where the NAv crash in the Savage Land is a ruin that Luke Cage says it's the place where the original New Avengers had their 1st battle, but it looks different now. He is presumably referring to the Mutates' base in NAv#5. But it already looked as ruined in NAv#6 as it does now. There's possibly some extra machinery there, but is this never explained.

Skrull-Jarvis disables StarkTech worldwide with a computer virus. MAv#15 explains how the Skrull-Henry Pym learned how to compromise StarkTech when Ultron did it in MAv#1-6. And MAv#14 shows Tony Stark giving Skrull-Jarvis complete access to the Avengers computer system, where he introduces the virus.

We never actually learn when Jarvis got Skrulled. But Dum-Dum Dugan was replaced in SI: Prologue, and MAv#15 covers the replacement of Henry Pym.

I have briefly described these and other events relevant to the build-up towards this Invasion in comments attached to SI Saga, SI: Who Do You Trust, SI Prologue and Illuminati #5 in that order.

There are several other issues which tie in to this 1:-
(The sequence of events in my comments on this series is based on the Marvel Chronology Project Forum thread here, but I have moved around some of the elements.)

Iron Man (2005) #33(p1-2:4) repeats the failure of Iron Man's armour, and of StarkTech in the SHIELD helicarrier (except it's moved from New York to the Bernmuda Triangle!) and the Raft prison symptomatic of the worldwide failure. It also includes StarkTech failure at the Initiative HQ and training base at Camp Hammond.
Av:Initiative #15(p4:4-7) shows the StarkTech failing in 3-D Man's quinjet, and crashing in New Mexico. Then it picks up the hint from this issue and shows War Machine affected, and he's saved by a power boost from Baron Blitzschlag.
MAv#19(4:6-5) duplicates the scene in the Cube here where the StarkTech failure disrupts the system by which Marvel Boy kept the guards and prisoners under control, and he decides it's time to leave and hunt Skrulls.
Punisher War Journal (2007) #24(p4-5) shows StarkTech failure at SHIELD Grey Box Facility 17 automated prison freeing Frank Castle. He stops to warn all the other prisoners not to try to escape or he'll kill them.

Thunderbolts #122 (p14-15) shows Swordsman explaining how he's given some of his skin to his sister Andrea Strucker so she can use their combined power. Then it interpolates panels of the scene from here where Captain Marvel starts to attack Thunderbolts Mountain.

SI:FF#1(p6-11) replays the Skrull-Invisible Woman opening the Negative Zone portal to suck the Baxter Building into it. Human Torch and Thing protect Franklin and Valeria Richards as they pass though. The top floors of the BB end up floating in the Neg Zone.

Nova (2007) #16-17(p1-3) The original Super-Skrull helps Nova against some of the new Super-Skrulls. Kl'rt tells him about the jihad approaching Earth, which he doesn't agree with. They arrive here at the same time as the Armada. Kl'rt pretends to kill Nova to infiltrate the Invasion, but actually protects him with a forcefield.
PWJ#24(p6-7) By the time Punisher gets out he sees the Skrull armada over Manhattan.
MAv#18(p21-22) Nick Fury and his Secret Avengers see the worldwide Skrull armada on viewscreens.
SI: Front Line #1(p1-15) Various people witness the armada over Manhattan. Johnny Bryant who's been having a bad day - he caught his wife cheating, and Spider-Man and Menace trashed his cab. Melanie Crane who visits her father Vincent in Avengers Tower, angry that her parents are going to divorce. Ben Urich who is interviewing Dr Molly Young in Empire State Hospital A&E.
SI:ASM #1(p1-13) While Spidey's off in the Savage Land this follows Jackpot and others of his supporting cast. She's in The DB offices with her Superhuman Registration Act union rep demanding an apology for the paper's libel about her. Dexter Bennett calls for the police. Then the Skrull spaceship arrives.
SI: Home Invasion #1(p15)-2(p1) When Kinsey awakes after the crash she finds herself alone in the car with the alien gun, and alien warships overhead. She staggers out of the car and collapses.