In order to add some clarity to events I will sort events by location and then in the approximate order they occur though some events are concurrent

Manhattan

• Iron Man gets Reed Richards and Hank Pym to analyse the Elektra Skrulls corpse
• Jessica Drew informs New Avengers of a Skrull Ship that has crashed in the Savage Land
• New Avengers and Mighty Avengers Depart for the Savage Land
• Baxter Building taken into Negative Zone by Lyja disguised as Sue RIchards
• Hank Pym Skrull “disables” Reed Richards
• Jarvis Skrull uses an Alien Computer Virus to disable iron man and all Stark Facilities
• Skrulls launch full assault on Manhattan initially only Young Avengers present
• The Void rescues Lindy from Skrulls attacking Stark Tower
• A YellowJacket (Hank Pym) Skrull orders the Initative Recruits into battle
• The Vision is disabled (head blown off) and Proton killed
• Nick Fury and his new howling Commandos arrive saving Annex from execution by killing a superskrull after clearing a zone of skrulls Fury shoots Ms Marvel as he cant be sure of her identity.
• The Hood orders his gang of villians to go out and fight the skrulls
• Thor and Captain America arrive at the scene of the battle

The Savage Land

• A Skrull Ship crashlands in the Savage Land
• New and Mighty Avengers arrive at Crash site
• Luke Cage opens ship leading to the skrulls commencing their assault
• Iron Man disabled by Skrull Virus
• “70s Heroes” emerge from ship and Luke Cage starts a fight with them which is broken up by a T-Rex
• Sentry flees battle to Saturn where he is “consumed” by the Void after the 70s Vision initiates a skrull plan to neutralise him
• 70s Spiderman (with Underarm webing) and 70s Hawkeye revealed to be Skrulls
• Clint Barton (Ronin/Hawkeye) vouches for 70s Mockingbird
• Iron Man taken to the Mutate Citadel by Miss Marvel who then departs for the mainland
• Spiderman (Potential Skrull due to costume mistake) runs into Ka-Zar and some mutates and Ka-Zar explains that it was the skrulls who were Vibranium mining (see NA#1-6 for details), 70’s Captain America then interupts their conversation. (NA#41)
• Spider-Woman attacks and severely injures Echo (possibly killing her) admititng her “skrulliness” and Echo’s humanity in the process
• Empress Spider-Woman finds Tony Stark and tells him that he is a sleeper skrull and one of the great heroes of the invasion
• The Black Widow overhears their conversation but is interupted by 70s Beast and Phoenix who she kills revealing them to be skrulls, but Spider-Woman gets away. She also shoots Wolverine (NA member not 70s version) who gives her the correct code word in response

Elsewhere

• Dum Dum Skrull disables SWORD HQ
• Captain Marvel skrull attacks Thunderbolts Mountain
• Breakouts commence at The Raft and The Cube
• Jarvis Skrull reaches the downed SHIELD Helicarrier and orders Maria Hill to surrender, the majority of the SHIELD agents on the helicarrier then reveal themselves to be skrulls 
• Captain Marvel Skrull defeats the Thunderbolts but is unable to kill anyone so Norman Osborn offers him a drink and a chat