"Beginning of the End" is the twenty-second episode of the ABC/Marvel series Agents of S.H.I.E.L.D. It premiered May 13, 2014.
Plot
In the Cybertek headquarters, Kyle Zeller, the head tech guy, introduces a new recruit to the control station. The recruit, much like others present are there for the incentives program. One of the operatives calls Zeller over to see a feed shown through the eyes of one of the super soldiers. The feed shows the S.H.I.E.L.D. agents being confronted by an army of super soldiers and a man armed with the Asgardian staff.
The agents engage HYDRA. May quickly disarms that man with the Asgardian staff and uses it to knock down the columns supporting the ceiling. The agents flee, leaving the building to collapse on the super soldiers.
John Garrett is unconcerned with this lost, but rather rips off the door to the Bus's lab and begins etching blueprints to a Kree city into it. Grant believes Garrett is going insane, but Garrett believes he is finally seeing more. Grant is concerned that HYDRA taking over is a bad thing, but Garrett claims he will give him anything he desires, because he can do anything, revealing a series of lines that he has drawn.
Skye is glad that her enactment of the virus worked. Coulson informs them that Fitz-Simmons successfully planted a tracker of the Bus to help them locate it, but the agents are wary that they cannot communicate with the scientists.
Simmons wakes up to a somewhat depressed Fitz, who has been thinking about how the containment pod they are in sunk. He broke his arm upon impact with the water and sees no hope for them to return to the surface. Simmons, however, remains positive. Fitz is even more hopeless because their beacon will likely not be picked up by anyone and they both believe they will not be saved.
Ward expresses his doubts in Garrett to Raina. She and Garrett admire the specimen of Gravitonium. She reminds him that Ian Quinn expects it as payment, and tells him of Ward's compunctions. Now that Garrett is seemingly all-knowing Raina asks him what she will become.
Fitz-Simmons, both scared, discuss death. Jemma takes hope that her energy will some day become a part of something bigger. They both realize that they could remove the window through detonation in order for them to escape their watery tomb.
Ian Quinn gives a continued presentation to the US military. Coulson and Triplett distract the HYDRA agents long enough to sneak up, knock out the bad agents, and steal a Humvee. They tear their way into the compound, giving May and Skye entry. Quinn must explain the security sirens to the military delegates, but Garrett, Ward, and Deathlok enter. The general demands an explanation, but Garrett gives him a demonstration: tearing out a portion of the man's intestines. Garrett tells them all that this is the beginning of the end.
Ward stops Raina as she tries to leave the Bus with the Gravitonium. She informs him that Skye is the next step in Garrrett's evolutionary theory.
May and Skye enter the control room at Cybertek. The men and women who have been controlling the super soldiers are scared by Skye's bomb and their prior knowledge of Melinda May. Zeller switches every soldier over to "Default Directive" which is to defend John Garrett at any cost. Coulson uses this to lead him directly to Garrett.
Skye calls Garrett to inform him of their takeover of the control center. May ushers the handlers out of the room. Garrett commands Ward to find May.
Fitz and Simmons are about to blast the window, but Fitz sadly informs her that she gets the only breathing apparatus to save her. He says he was never able to tell her that she was more than a friend to her and he wants to show her now. He quickly presses the button and the container floods with water. She swims to the surface, towing her unconscious friend. Both are rescued by a man in a helicopter: Nick Fury.
Simmons awakens in a decompression chamber on a jet. Fury informs her that Fitz is alive but only barely. He asks if she has any way to get to Coulson and his team.
Skye is confused as to why Zeller and the other handlers would be willing to die for HYDRA's sake. She asks if it is due to the incentives programs. Ward enters telling Zeller that Skye is not likely to kill him, because she is noble. She calls Grant weak for betraying S.H.I.E.L.D. He claims that Skye is the one who forged the weakness inside of him. Skye informs him that she has a weapon more dangerous than a bomb for him: the weapon is dangerous because he slept with her. Ward is immediately tackled by May. She fights him in a side room containing saws.
After Triplett creates a distraction, Mike Peterson leaves Garrett alone. Phil issues a single punch before being hit across the room by Garrett. When he looks up, he discovers Nick Fury. Coulson tells the former S.H.I.E.L.D. director they will have a heated discussion after the resolution of this battle against John Garrett. Fury hands Coulson a large gun which creates massive concussion pulses. Fury shoots Garrett several times, but the HYDRA agent is unphased.
Ward and May continue to fight as Skye forces Kyle to tell "what [Cybertek] has on him." Garrett is surprised to see Nick Fury and babbles on about the future which he has seen and believes Coulson to have seen as well. May nails Ward's foot to the floor and punches him, damaging his larynx. Kyle is reunited with his wife and begins unlocking doors until she finds Ace Peterson. Garrett points for Deathlok to execute Coulson and Fury, but Skye asks for Ace to type a message to his dad. Upon receiving this message, Mike turns against his former master. He steps closer to Garrett and stomps his skull.
The super soldiers are led away to have the backscatter eyes removed so that they can return to normal life. Coulson tells Ward that his life will be filled with torture because of his attempt to kill Fitz-Simmons. Mike watches the compound and his son. Skye asks why Mike has yet to go to his son. Mike says he does not want Ace to see what his father has become. He refuses to be taken in by S.H.I.E.L.D. because he must make amends.
In a S.H.I.E.L.D. lab, John Garrett attempts to heal himself using Cybertek-designed prosthetic implants, but Coulson blasts him with the particle cannon.
Coulson is incredibly angry with Fury for bringing him back, despite Coulson's own wishes. Fury gives Coulson a cube, called the "Toolbox" and informs him that he is now the director of S.H.I.E.L.D. to build it back up. Fury informs May and Coulson that he will be stepping back to relax but he will still be everywhere.
Simmons returns to the plane after Coulson follows coordinates on the toolbox. She tells them that Fitz is alive. They are informed by Agent Billy Koenig (who is identical to Erik Koenig) that they are at a secret base which he calls the Playground. He asks where Coulson would like to begin.
Raina enters a dark building. She shows a picture to a mysterious man. The man picks up the image which is of his daughter as blood drips from his skin.
Coulson, unable to sleep, admires the etching Garrett had formerly done. From memory, he is able to recreate the same images on a nearby wall using a pocket knife.
