Ok, this is my first post and I hope I'm doing this right. Before I say anything, I just want to say that this is my crazy theory that I will try to support as best I can, but in no means 100% set in stone, will happen and in the script, but rather a figment of my imagination, so here goes...
Back To Season 1
We all remember possibly the best reveal as to how Eobard Thawne was Harrison Wells. I'm halfway through The Flash season 2 and I still can't get past it. That device basically changed everything about Eobard which led to the messed up timeline where STAR labs exploded a couple years ahead of schedule. Remember this machine because it will come into play a bit later.
Now we know everything that happened next like Reverse Flash's reveal and the epic fight where Eddie killed himself, (a vacectomy would've worked just as well but he wanted to play the hero or something). But after all that, the breaches opened up and then at the start of season 2 Jay Garrick appears.
Que Jay Garrick:
But what if he's not who he says he is? See we've just accepted that he doesn't have his speed so he must be telling the truth, just like Harrison Wells wasn't Reverse Flash because he was wheelchair bound. That brings me to the Reverse Flash episode where Harry says something along the lines of this being his origin story. Now I don't know what story line they are using in the series but the comics was a bit different, but this is where my theory comes in...
Eobard hearing that he has already been defeated, but getting back to the future with the help of Barry, has a different plan. From Eobard Thawne's time they know alot more about alternate Earths and breaches beacause they are much more advanced. Now I don't know what wil happen if Eobard changes some things and doesn't turn into Harrison Wells, but the timeline is already broken and fractured so that makes his exsistence an anomaly. Eobard then using his machine, knowing about the breaches, turns into Jay Garrick and pretends that he is from Earth-2 and appears about 6 months after the breaches as the Jay Garrick we know and love. Which brings me to another part of my theory and that is the man in the iron mask. I think that is Jay Garrick and that Zoom stole his speed because of the reaction after tapping J-A-Y on the glass and Barry telling him he's back on Earth-1. Meaning that Zoom knew that wasn't really Jay on Earth-1 and then killed him anyway. So we might see the real Jay again because I don't think those breaches will stay closed. And that was my theory, but it has a few holes in it so be gentle guys.
The Flash season 2 continues Tuesdays on The CW.