The team discovers Turtle is dead and Jay suspects Dr. Wells is responsible. This is a low blow for them since they just lost the one thing that could help them defeat Zoom. Now it is back to the drawing board. Caitlin is also tries finding a cure for Jay’s illness.
Meanwhile, Cisco asks Dr. Wells for help in controlling his vibing abilities. Harrison determines they are connected to Cisco's fear response and triggers a vibe which alerts the team that Eobard Thawne is back. This plot is leaving viewers, and now the team, wondering how can Thawne be alive. In the season one finale the timeline should have drastically changed when Eddie killed himself. Wells surmises that this version of Eobard is from a point in the future before he went back in time to kill Barry's mother and was thus protected from being erased with Eddie's sacrifice. So Reverse-Flash own future timeline still existed, and that allowed him to continue to hunt for the truth of the Flash’s identity, and all of the events of the first season.
Retrofitting goggles to induce Cisco's vibes, the team learns that Eobard is planning to use tachyons to return to his future. Barry arrives and destroys Eobard's tachyon machine. After a race around the city, Barry stops Eobard and imprisons him at the particle accelerator. However, his capture causes a rupture in the timeline that threatens to kill Cisco, so Barry is forced to send Eobard back to the future to save his friend. These events lead to the revealing that it’s Barry who put into motion the events of the first season and the death of his mother. Had Barry never captured Thawne at this point in time and had a chat with him, then Thawne wouldn’t have known Barry’s identity. Now Barry knows that he’s the one at fault for everything that’s happened. This means Barry will never move on from Reverse-Flash.
Patty is still around despite her announcement in the previous episode. It would appear that she told Barry she would be leaving Central City as a way of testing him. To see if the relationship was going anywhere and if Barry really wanted what they had. Only Barry did the opposite of what Patty was hoping he would do and told her to leave. Patty insists that she and Barry talk. Patty goes through old cases and pieces it together that Barry is the Flash. Only Barry refuses to acknowledge it. This doesn’t seem to bother Patty too much, well at least not at the end of the episode when she gives a false distress call to Barry in hopes that the Flash will come to her rescue. This is just a ploy that Patty does to prove to herself that what she believes is true since no one wants to admit it to her. A ploy similar to that from Lana Lang’s book on Smallville. Patty is successful in her attempt but considering their audience, plays it off with the reassurance to not spill the Flash’s secret.