So, here's how it ends.
* Janet begins turning in to a biological weapon, making human and Skrull alike violently ill. Thor is forced to kill her to stop her.
* With their final weapon defeated, the Skrulls panic, not realising that what they'd done to Janet would only serve to anger them. Wolverine charges Veranke and is about to kill her when Norman Osborn shoots her through the head.
* Stark arrives back in the fight in an old armour not connected to any computer system.
* The Skrulls are left in disarray. The humans who are able to fly, along with Ares start attacking their warships, forcing the Skrulls to surrender.
* The last warship is brought down and is found to contain Hank Pym, Elektra, Mockingbird, Spider-Woman, Dum Dum Dugan and everyone else the Skrulls had captured and replaced.
* Jessica Jones notices Jarvis amongst the prisoners and realises what she had done. She desperately returns to Avengers tower to find Jarvis and her baby gone.
* The Hood's gang are allowed to leave quietly for their efforts in defending New York.
* Thor tells Stark that he meant it when he said he would never fight alongside Stark again.
* In the aftermath, the President begins a review of events. He removes Stark as Director of S.H.I.E.L.D., disbanding the entire organisation and ordering that the US military is not to use Starktech any longer. An investigation is to be begun and Stark faces criminal charges.
* Stark's replacement is Norman Osborn as head of the Initiative. Osborn goes to Avengers Tower and meets with some people...