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I'm a bit confused as to why they would be so quick to close the portal if all the Chitauri were powering down/dying? What's the big rush?
I think the only thing that could make sense would be the nuke blast coming through the portal, but the explosion seems way too far away to have done that?
They did not know what else was coming. There could have been a huge alien about to come through which they could not have stopped therefore they had to shut the portal as quickly as possible even if it meant sacrificing Stark (who, btw, proved that he was the one to make the sacrifice play after all).
I always took it as protection of the city from the radioactive fallout of the nuke that just detonated on the other side.
Also, another explanation could be that no one was watching the troops since they were concentrating on the portal, so they didn't know at the time that they were all dead.
This was because of two reasons.
The Portal was still spewing oodles of Chitauri. The Avengers did not know that destroying the mother ship would neutralize all the Chitauri. That was a last resort to handle the Nuke. Nowhere is it shown that Tony was aware of this neural link prior to him pushing the nuke through the wormhole. This was their last action plan... To nip it at the bud, so that they could take out the Chitauri still remaining in the city. Their primary plan was to close the portal. This is clear through several pieces of dialogue:
Captain: Alright, listen up. Until we can close that portal up there, our priority is containment.
Then we have:
Captain: Thor, you've gotta try and bottleneck that portal.And Also
Black Widow: Captain, none of this is gonna mean a damn thing if we don't close that portal.
To save Manhattan from the massive amount of fallout and debris falling through. Manhattan would've suffered even more casualties had the tons of debris fallen through.
I understood it to be that they didn't know that sending the nuke through the portal would actually affect the Chitauri or even stop them as it did. Therefore they only thought that closing the portal would make the difference. Tony didn't know that when he flew the nuke through there and neither did Black Widow.
If the distance between the blast and the portal was small, then it could have come through, so it would have to be closed as soon as possible. If the distance was large, then other Chitauri, not killed in the blast, could have come through.
