Back in 1983, Jiaying (Skye's mother) is seen comforting a boy named Gordon, who has just gone through Terragenesis. She reassures the blind teleporter everything will be fine by saying, "It's okay beautiful, I'll show you the way."
In the present, Skye is locked in quarantine struggling with her transformation and the guilt of Trip's death. Coulson attempts to comfort her by assuring her Agent Triplett died a hero. "He may have saved all of us" the director tells Skye.
Though everyone was dealing with the loss in their own way, most of the agents went back to work.
In Puerto Rico, Simmons was preparing to flood the ancient city's tunnels to prevent any further contamination. Raina resurfaces and kills several agents gathering's samples from the ancient city. Simmons attempts to shoot Raina and sees that her DNA changed; she now has porcupine quills.
Meanwhile, Hydra leaders meet to decide who will replace Daniel Whitehall. It's agreed that whomever does away with S.H.I.E.L.D. gets the job.
On the bus, Mack argues with Fitz telling him, "You know what it's like to lose control? To be trapped inside your own body unable to tell it what to do? To watch yourself hurt the people that you care about?" Fitz replies simply, "Yeah" and Mack realized Fitz is right.
The team gets together to plan their next move and Mack again becomes aggressive, this time toward Coulson. He blames the director and Skye for leading the team down into that alien city over their obsession with the alien glyphs.
Skype begins to get agitated and the quarantine room began to shake; she frightens herself.
S.H.I.E.L.D. strikes a deal with General Talbot to turn over Bakshi in exchange for military assistance stopping Hydra. However, this was all part of Coulson's plan to have the villain lead them to Hydra and finish them off once and for all.
After a massive shootout during Bakshi's transfer, Coulson and May appear to be killed. Hunter, in Hydra agent attire, rushes Bakshi away from the scene to a Hydra safehouse.
Elsewhere, Raina and Cal meet and she begs for his help with her condition. She explained she's in terrible pain from the thorns. He smiled and replied "You always did like flowers." Poor Raina is pretty much on her own as Cal's bent on revenge. He plans to kill Coulson for denying him his vengeance against Whitehall.
Simmons and Skye catch up and the scientist mentions that Raina's DNA has been altered. She tells Skye this could possibly be the start of a some type of plague. They needed to make sure Skye's blood samples were clear.
However, Fitz figured out that Skye had indeed changed as well. Though he explains to her that her heartbeat monitor read almost 300 bpm during the temple collapse, he decides to release her from quarantine. If she's clearly "inhuman" now, why lie to everyone and set her free?
Ultimately, Hydra's leaders are assassinated one by one, and Bakshi is turned over to Talbot, as originally promised.
A distraught Raina attempts suicide by walking into traffic, but Gordon teleports in to save her saying, "It's okay beautiful, I'll show you the way."
Bobbie and Mack discuss their secret plans, and in the final moments we learn they have something to do with Fury's toolbox.