Clearly, Nora made a deal with
Spoiler
Thawne. He helps her shift the timeline to save her father and in return, she timehacks a way for Thawne to survive using Sherloque's body.
Every Wells has a tragic ending in Flash and who had the idea to bring in a Harrison Wells from another Earth? Bingo. The person working with Thawne in the future; a Thawne who looks like Harrison Wells with longer hair and chin scruff just like the Wells from this season. Wasn't the idea of a time hack conveniently introduced this season? And Sherloque has started to decode the speed force writing - which judging by "This house is bitchin'," is all linked to Nora and by extension, Thawne. (It's also the Book of Destiny's writing.)
You know, TBH, in comparison to Arrow...
Spoiler
With pretty much the exception of the prior week(to Elseworlds), and of course Legends of Tomorrow, but definitely not on the main show, the main villains on Flash never come back. In Arrow, Merlyn came back in pretty much ever ensuing season. Deathstroke also came back for special episodes and even had his own arch. Understandably Ras and Prometheus haven't come back, Diaz, the big bad from the prior season is seemingly the big bad for this season. But in Flash, Season 1, Thawn. Season 2, Zoom. Season 3, Savatar. Season 4, Thinker. Defeated. Defeated. Defeated. Defeated.
And the issue with me is, as it is in the comics and as they consistently allude to in the show, these villains often pop up to give heroes problems, but in the Flash they just get beat and seemingly go away forever. It'd be nice to see, at least some of the bigger ones come back a few times here or there, if not for a whole other season.