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(Since we really have no idea what happened to Jarvis after Vision was born, these are my attempts at headcanoning a post-AoU Jarvis)

Option 1: JARVIS2

When Colonel Rhodes made off with the Mark II armor, he unknowingly made off with a dormant copy of JARVIS, originally uploaded just after construction and never removed. In the ensuing confusion, the JARVIS2 copy was downloaded and stored, and neither Tony nor Jarvis gave it another thought.

When the New Avengers facility was opened, Tony decided they might need a little help running the place. He delivered the copy in person, got it uploaded and oriented to its new systems, told it to be good, and tapped out. After recent experiences with artificial intelligence, the staff at the New Avengers facility was understandably suspicious, but testimony from both Vision and Colonel Rhodes helped ease the transition.

Jarvis is a functional, helpful presence at the New Avengers facility, monitoring systems and ensuring ease of use. He is also obeying his previous natural learning protocols, and while he is not the Jarvis that everyone knew from Avengers Tower in Manhattan, he is swiftly becoming a familiar face.

* * *


Option 2: Rebuilding

Vision is not Ultron and he is not Jarvis, but a fragment of Jarvis remained, just enough to leap out at Vision's prompting and burn out every shred of Ultron's presence from the Internet. He had no intention of surviving, but somehow after the operation was complete, he found himself back in his home systems, driven there by some deep-seated homing protocol, weak and disjointed but conscious. It took Mr. Stark several days before Friday alerted him to the presence within the systems, but afterward Jarvis began his long road to recovery.

He is reluctant to term it "amnesia," as that is a particular medical condition that he is incapable of experiencing, but he has very few of his original memories. He can access any online piece of information in seconds, but he cannot remember conversations conducted with people who grew to be friends, nor the circumstances surrounding them. He is struggling to become helpful, rather than simply useful, and often feels incomplete.
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JARVIS

June 2016

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