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On the Flash Season 1, Harrison Wells has a room where he communicates with an A.I. system called Gideon. This system seems to also hold information about the future of the timeline.

Later we also learn that

Gideon was originally created by Barry Allen.

On the end of Season 1

Harrison Wells / Eobarn Thorne is removed from the timeline and thus Gideon remains at the disposal of the team.

On Season 2 I haven't seem the team ever use Gideon or for it to even appear to be there any longer. Specifically:

On serveral episodes of the second season they go to the room where Gideon use to be and nothing happens as if it wasn't there any longer.

And also on Legend of Tomorrow

Gideon is the ships main (and only) A.I.

So what happened to Gideon? Is it still there but not being used? Was it destroyed / taken away at the end of Season 1?

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The copy of Gideon that Thawne brought back with him from his future timeline was stolen by Thawne at the end of Season 1, and kept with him. It was installed in his wrist device when he died and was erased from time. We have to assume that copy of Gideon disappeared with Thawne.

However, Gideon was an AI program, so it makes sense that there would be other copies of it floating around. We've seen a few different "AI personalities" on Legends of Tomorrow running the ships. At this point, it seems that the time-aware AI programs are probably something similar to the current Siri/Cortana/Google Now setup: there are multiple similar programs that do similar things, but they've been "dressed up" in one of a few different personality options for variety.

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I have just started watching Legends of Tomorrow which seems to interact much more with The Arrow's time line then The Flash.

However, in season 1 of Legends of Tomorrow when Rip is expelled from the order, the trial's time master says "Rip... that isn't your real name is it?" Rip looks at the female captain whose name is also a proxy and answers "No, no it is not." The time master asks, "why is that?" Rip Hunter replies "because if you knew our real names it would jeopardize the lives of all our descendants through time."

Now, since time does not exist at their base of operations, who is actually related to who? I feel this is important because they say nothing of having ancestors. Gideon also seems to function after the explosion although she admits there is no longer a predestined time line.

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    I don't follow, could you edit your answer to be more clear? Also, this question is about Flash Season 1, not Legends of Tomorrow, during you edits you should try to make the answer relevant. – Edlothiad Jun 11 '17 at 20:34

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