I'm thinking this is Thawne's mindset here...
Far in the future, Thawne, much like his comic book counterpart, is captivated by stories of the Flash and begins building a suit that can replicate his power. He eventually creates one and becomes the Flash of his own time, but much like Barry in this last episode, at some point, he goes so fast that he travels back in time. Thawne attempts to return to the correct time by going faster and faster, but he realizes that he can only go back in time and not forward. This has been a common theme in certain time travel stories; you can't go forward in time because the future hasn't been made yet; you can only go backward (Timecop, Quantum Leap).
Eventually, he finds himself in the year 2000 and attempts to kill young Barry Allen, theorizing that by doing so, the Flash will never have existed and thus he will have never gone back in time. The plan backfires though as adult Barry arrives and fights Thawne, which results in Barry's mother getting accidentally killed.
From there, Thawne realizes that he has inadvertently put into motion the events that would create the Flash. He therefore begins work on the particle accelerator to complete the creation so that he can perhaps siphon power off of Barry somehow and find a way back to his own time.