So, in season one of "The Flash" Barry Allen was struck by lightning and gifted with incredible speed. He proceeded to use his powers to bring down other metahumans created by the particle accelerator, all under the supervision of Dr.Harrison Wells. Wells turns out to actually be Eobard Thawne, or as many know, "The Reverse Flash." At the end, his great great great whatever, Eddie Thawne, shoots himself to prevent Zoom (Reverse Flash) from killing Barry, thus creating a paradox where Eobard never existed. This created a black hole that sucked everything, including Barry, into it.
This extremely long recap begs the question "what happens next to the Barry?" There is no definitive way to say without knowing the script, but from what I can guess, it's going to be crazy, especially since in comics, Barry was the first to go to parallel universes. I think it will be a universe where Caitlyn is bad and becomes Killer Frost, and a universe where Thawne didn't die. This also means that there will be a second Flash, probably Jay Garick, based on his helmet being thrown out of the time loop. I'm guessing that they will combine forces to defeat Eobard Thawne, who is backed by Killer Frost.
The universe will have a whole 'nother set of characters, and Cisco from the original universe will know all that is going on, due to his ability to recall what happened during the timeline where he died. He will probably try to get Barry back to his proper universe during the course of the season. This is my guess for the second season of "The Flash," be sure to leave your thoughts in the comments.