So this is just to clear some things up about the good Professor, just to lay everything out on the table and try to get it all straight going forward. There's a lot of stuff going on where he's concerned, so I want to make sure I've got it all right as we head into the grand finale. Last spoiler warning before I dive in.
Still here? M'kay:
So let's start off by getting the timeline/circumstances straight: In the year 2020, Harrison Wells and his wife Tess create a particle accelerator that backfires, empowering all kinds of people, one of them being Barry Allen, who gains a connection to the Speed Force, and of his own means somehow becomes the Flash, complete with suit. In the 25th Century, Eobard Thawne somehow gains Negative Speed Force abilities, and travels back in time to fight the Flash. During a Crisis, Barry corners Thawne, who travels back in time to when Barry was a child, hoping to kill him before he can ever become the Flash. Barry successfully saves his younger self, though his mother is killed by shrapnel from the fight thrown at superspeed. Meanwhile, sent running from the fight, Eobard crumbles, his powers exhausted. Eventually he kills and takes the form of Harrison Wells to accelerate the timeline, hoping to get back to the 25th Century and restore his powers.
As for Eobard/Well's scheme, thus far, it was, as I recall: Get Barry powered up, start coaching him, training him, get enough fuel in Thawne's tank to let him engage Barry directly. Use that encounter to taunt Barry about his mother's death, beat him down, using that encounter to give Barry a real reason to start pushing his limits as fast and hard as he can. Meanwhile, exploit Joe's protective and cop instincts to convince him to keep his cards under the table and investigate quietly, rather than immediately bringing his suspicions to Barry. Doing so gives Thawne more time to build up power, and trust between him and Barry. When Barry's ready, and on the verge of performing a timejump (heralded by parallel deja vu, which Barry would obviously tell Wells about), kill whichever of the STAR Labs members is closer to discovering the connection between Wells and Reverse-Flash, knowing that Barry post-timejump wouldn't be able to resist changing history and thus giving the killed member dreams of their traumatic death. Subtly guide the investigation to uncover the dreams, making sure to have recovered Everyman (who Thawne would know about as a member of the Rogues) by this point, let them set up a trap, release Everyman, give him the script, make the grand escape.
As for why he's going to all this trouble to get Barry up to speed when he apparently hates him so much (most of this is speculation based on the comics): Thawne, as in the comics, uses the Negative Speed Force, hence the inverted colors. The NSF draws it's energy from the real Speed Force, which Barry is inextricably linked to: It lets him run fast, and as he runs, he generates more of it. In turn, the NSF grows in power directly equal to the SF. The equal/opposite reaction, so to speak. By the 25th Century, Barry's run most of his life prior to dying. And more than likely generated other Speedsters also fueled by the Speed Force. So the NSF, untapped til then, is pretty full. Thawne taps into it, and starts time traveling to fight Barry, generating more fuel for himself. However, when he traveled back in time to when Barry was a kid, there was no Speed Force, due to Barry not yet having his powers. He was able to keep going for a bit since Future Flash was right on his tail, but Thawne quickly started to run empty, which was only exacerbated after Future Flash left and what energy their fight had generated quickly ran out. So now he's getting Barry up to speed to fuel his own powers and get home.
If you've read all that, a genuine congratulations to you: Have I got it all right? Am I missing/forgetting anything? Have I got anything wrong? If so, please correct as necessary.
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