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Fury is ordered to capture Spider-man so that S.H.I.E.L.D. can discovery how he got his powers and see if he is a menace to the world. Against his better judgement he orders the Avengers to do so. In the process they discover how young he is, and that the people of New York are NOT okay with that idea, not at all.

During this they also discover the reason they were ordered to do so, was mainly because they wanted to see why Spider-man had been able to become a hybrid spider/human cross, when experiments with others human/animal failed. When these experiments escape and start killing people, a cure is found that will kill the hybrids.

Spider-man does the heroic thing and releases the cure across the city, knowing that it will kill him as well. As he is dying he makes it back to the tower to say goodbye to the team.

I think I found it one time on Archiveofourown, but search has failed me.

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From:

maskshredder.livejournal.com

It wasn't on Archive of our own I don't think, but I think the one your looking for is The Humanity of Spider-man on FF.net

https://www.fanfiction.net/s/10519888/1/The-Humanity-of-Spider-Man

From:

cliff stamper (from livejournal.com)

yes, this is it, no wonder I couldn't find it. (Thumps head on desk)

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Avengers sent to capture Spirder-man