We have seen a lot of theories about the Reverse Flash around the web. It is still a mystery as [The Flash](series:1068303) continues to confuse us with every episode. I'm not gonna waste much of your time. So here we go:
In the beginning of every episode what does Barry say?
"My name is Barry Allen, and I am the fastest man alive. When I was a child I saw my mother killed by something impossible, my father went to prison for her murder, then an accident made me the impossible. To the outside world I'm an ordinary forensic scientist, but secretly I use my speed to fight crime and find others like me, and one day, I'll find who killed my mother and get justice for my father. I am The Flash!"
Oh yes, you read that right:
"I saw my mother killed by something impossible...then an accident made me the impossible."
That is not just a thing to simply ignore.
If you have seen The Flashpoint Paradox you will understand. I believe this show will have a similar story.
By the latest episode of The Flash - S01E14 - "Fallout" we have come to know many things like The Yellow suit Being in Dr. Wells' possession, that the tachyon prototype is used to separate Ronnie and Stein, and also that *SPOILERS* it's Dr. Wells in the Yellow suit. Revealed! We also know that Barry has learned that he would one day be able to travel through time and that he HAS PLANNED to go back in the past and save his mom.
Now comes the theory
I think that Barry is able to go back in the past and save his mom but he breaks the time barrier and creates a new world, changing the timeline where probably nothing like the original one exists and maybe the world is at its end. After realizing everything, he decides that the cost of the life of his mother was unacceptable. At this point he decides to return to the past and stop himself from saving his mother. He knows now that he is no longer Flash but the Reverse Flash, and he has to kill his own mother to prevent this day from coming. As Barry now has learned to break the time barrier he is Reverse Flash, who obviously is faster than The Flash. So Barry as the Reverse Flash goes back in the past to stop Flash from saving his mother, but the Flash seeing him thinks that he has finally come to kill his mother and they are at war.
In between the fight among them trying to save Nora Allen and at the same time the Reverse flash trying to stop Flash, one of them probably gets hit and his blood is splattered on the wall which we have already seen. The Reverse Flash i.e the present Barry is able to kill his own mother and save the world at the cost of a life. He probably gets away with the murder and The Flash loses him. Perhaps, Flash returns to his own timeline but the present Barry (Reverse Flash) whose world no longer exists goes to Harrison Wells, explains the situation and teams up with him. We have already seen Dr. Wells being suspicious all the time but we do know that he is a good man. The particle accelerator was made to explode, as hinted in the "Fallout" episode. Dr. Wells believes Barry's story and decides to go along with him.
But the question arises, 'Where is Barry?' Barry being missing and Dr. Wells being seen running at the Flash's speed shows that they have been merged, just like the Firestorm. This also explains Dr. Wells getting beaten up by the Reverse Flash. They may have made an agreement to do this so that Dr. Wells is out of the suspicion list. Reverse Flash has a gift but he never uses that to do bad or good to the people. Why is that? 'Cause perhaps he knows that The Flash is the one who has to save the city. He has just done such things to bring the world to such a position where he himself is the hero and that everything happens as he wants. The tachyon prototype may have been used to merge Dr. Wells and Barry, as we have seen Dr. Wells run like that, and also it could have been used to separate them, when Dr. Wells was beaten. And as far as the part where Dr. Wells keeps looking for the Flash in the future is concerned, that "Flash missing, vanishes in crisis" also supports that, as Barry is now living 'in' Dr. Wells and no longer 'exists.'
So here we come to the end of the theory. Hoped you liked it. It was my first one so it may have a number of loopholes. Please point out your doubts. Thank you for reading.
EDIT - ADDITIONAL CONTENT TO SUPPORT THE FUSION :
People are still having doubts about the eyes of the Reverse Flash and that during the merging process, it requires a 'fitter' body and a 'healthier' mind of the host to survive.
Well this is actually not entirely true. Whenever the firestorm merged correctly (Balance of the mind is maintained), Ronnie has put the prototype on HIS BODY before the merge, the mind is equally shared by the firestorm. So if that maybe the case of the Reverse Flash, then probably Dr. Wells puts the prototype on his body before the merge with the Flash (from the future). So after the merge, mind maybe equally shared, but Dr.Wells' body remains the host.
And for the eyes of the Reverse Flash, where people are bringing the 'Rainbow Raider' (the meta-human who can hypnotise others with the red flashing of his eyes) into it, If you've seen FIRESTORM closely, you would notice that after every fusion or merge, the colour of the eyes are changed, they become white. In the Reverse-Flash's case, they probably become red. So this explains it I guess.