This season two premiere episode, named “Wake Up Call,” starts off with a quick rundown of season one. It is immediately followed up with Dr. Rosen having been put into a mental institution. Within seconds, he reveals that it has been eight months since he revealed the existence of Alphas to the world and is promptly returned to his room after his “session” is up. His rooms’ wall is lined with newspaper clippings of Stanton Parrish (Possibly the original Alpha; was hinted at being immortal last season).
We are quickly thrown into a sting operation being followed up by Hicks and Harken. Turns out that they are part of an Alphas crime unit where they are trying to stop crimes before they happen and then imprison those violent Alphas. Hicks and Harken don’t have all the Intel they need going into this fight (because they end up having to face Alphas that can act as conduits for electricity, push their bodies lie Bill Harken and even have banshee type powers) and end up losing two of the perps. While trying to bag the two on their getaway, hicks is revealed to be having troubles with his ability, specifically in focusing.
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When they get back to the office, it is revealed that Gary has been missing for the past two weeks from the NSA. The team doesn’t even blink. Things have obviously changed at this point as they reveal Rachel is a shut-in and Nina is pushing everyone she comes in contact with as if they were never part of the team. Hicks and Harken are now at Binghamton to drop off the Alpha they caught during the heist.
This is where we are brought up to speed about the chips being put in Alphas to put them into a vegetative state of mind. Harken recognizes Gary and immediately tries to save him. Clay lets them know that he has no say in who comes and goes and that Gary is there because of the government. Cut scene to Dr. Rosen being visited by his daughter who clarifies his mind of the drugs he’s been given. 
He tells her that he is just waiting for the coming storm that the government will let him out because they can’t contain the truth. BAM! Catalyst! The girl from the heist is getting a chip put in her when she back fires the entire chip system, bringing the violent Alphas out of their clouded state of mind. This all happens while Harken is trying to get through to Gary so, naturally, Harken is now being attacked by people he’s put in prison. Gary and Harken are now taken hostage and it seems that Scipio (an Alpha with the ability to burn people with his hands) is behind the coup.
The stars of Alphas discuss the show at San Diego Comic-Con
The storm has arrived! Clay is forced by Scipio to bring Dr. Rosen out to Binghamton. Although he was reluctant at first, Dr. Rosen agrees after hearing the whole story. It’s time to unite the team! Dr. Rosen recruits Rachel and Nina back to the team and they head to Binghamton. The whole time, Harken is trying to get through to Gary because he hasn’t said a word and isn’t acting like regular Gary. When he does talk, he lets Bill know that the team is there. Upon arrival, you can tell Hicks and Nina ended on bad terms with his remark of her having to push everyone she meets and her remark of him wanting to fall of a building. Dr. Rosen explains how he only wants the team to come in if the worst scenario starts to happen.
It seems like a good plan until you see Dr. Rosen in the middle of all the inmates. At that point, it feels as if Bruce Wayne had just entered Arkham Asylum with none of his wonderful little toys. It just got real. While talking it over with Scipio, Dr. Rosen feels as if he is being stalled and starts to wonder, out loud, whether or not this whole thing was staged by Stanton Parrish. This is when Scipio is told that everything is ready.
The captured team is brought to the front of the cameras for the rest of the team to see. They are lined up as if put on a firing squad. One guard is shot as Hicks goes into action and tries to get there in time to save his teammates. But it is too late as Dr. Rosen is burned alive by Scipio on the TV!!!
WHAT IS GOING ON!? Nina is freaking out but Rachel seems to be calming down when she tells Nina that she can’t smell the flesh or anything. Nina relays the message to Hicks, letting him know that the feed must be fake.
Hicks finds the electricity manipulating Alpha and “pulls the feed”. It was all a diversion tactic for the inmates to get loose! They rush outside in time to see the hostages getting away. Rachel starts to lose it when Nina pushes her to calm down. Gary and Bill are taken hostage while Dr. Rosen is left there because he isn’t one of “them”. Dr. Rosen can’t lose Gary and Bill and asks Hicks to take the shot. Rachel hears which car they are in and lets Hicks know. Hicks can’t take the shot though because he can’t focus. At least not until Dr. Rosen calmly reminds him of the quarter shot. He takes the shot and the car flips. Gary and Bill come out safe.
Clay is now talking to Dr. Rosen and he is letting him know that he can have his team back. But Dr. Rosen wants a few conditions met. Simply stated, he wants everything to go back to the way it was before he was committed. Clay quickly reminds him that he needs to play ball because, at any time, the government can institutionalize him again. Dr. Rosen is now forced to clean up the governments mess. The teams new assignment? Recapture all the inmates that broke out of Building 7 at Binghamton.
Cut scene to everyone standing around Gary and wondering why he still isn’t talking. He’s been silent since the crash and no amount of coaxing has had any effect on Gary talking. Bill tries and is on the right track by talking about his routine. Dr. Rosen jumps in and tries to nudge him in the right direction by letting him know the time of day and what he would usually do if he were just sitting there after a case. Gary is now talking and has a few choice words to say to the team, but he seems to be back to his old self.
The team is back together.
Now we see Stanton Parrish talking to Dr. Rosens’ daughter on a bridge. Stanton blatantly states that he is over a hundred years old by reminiscing about the Civil War. He is working towards a new world where Alphas are all that there is. A war is coming. Stanton turns around to see Scipio and others that were broken out of Building 7.
He now has his own team of Alphas.
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