Whitehall and Coulson's forces take part in an explosive confrontation that changes everyone. Skye uncovers some truths about her past.
- Immediately following the events of "...Ye Who Enter Here", S.H.I.E.L.D. Agent Melinda May outmaneuvers her Hydra assailants and flies to San Juan, Puerto Rico, where S.H.I.E.L.D. must race to enter the hidden Kree city below and destroy it before Hydra can get to it. A contact in San Juan reveals to agents Bobbi Morse and Lance Hunter that Hydra has already arrived, setting up residence above the ancient temple said to be needed for an extinction-type of event. Guessing that Hydra intends to drill straight down to the temple, S.H.I.E.L.D. decides to attack straight away.
Inside the Hydra base, former S.H.I.E.L.D. agent Grant Ward delivers his prisoner, Agent Skye, to her father, who introduces himself as Cal. He is regretful for having not been able to raise Skye and protect her himself, but wants to fix that now by helping her fulfil her 'destiny'. He explains that her mother came from a line of people who have gifts, and she was taken by Hydra agents under the guise of S.H.I.E.L.D. Hydra leader Daniel Whitehall butchered her, took the secret to her gift (long-life) and threw her remains in a ditch, where Cal found her, and swore vengeance against Whitehall, the man he is now supposedly aligned with. Realizing who Cal and Skye are, and that Ward isn't loyal to Hydra, Whitehall has the three incapacitated and guarded, but is prevented from taking further action when S.H.I.E.L.D. Director Phil Coulson attacks the base, along with May, Morse, and Hunter, in hopes of disabling the drill before Hydra can reach the temple with the Obelisk.
Agents Antoine Triplett, Jemma Simmons, and Leo Fitz enter the city and place Howling Commando explosives around the temple, ready to destroy it for good. During the fighting in the Hydra base, Cal escapes and finds Whitehall, ready to take his vengeance, but is prevented from doing so when Whitehall drops dead, killed by Coulson. Enraged, Cal attacks Coulson, and only stops when Skye threatens to kill him. He agrees to leave, and reveals that Skye's real name is Daisy. Agent 33, feeling lost without Whitehall, who had brainwashed her, helps Ward escape from S.H.I.E.L.D. and Hydra. Skye, wanting to make things right, goes looking for the Obelisk, and realizes that Raina, who Cal also believes to be descended from the gifted people, has taken it down to the city. There she finds Mack, possessed by the city, who guides her to the temple. Skye follows Raina into the city, and Coulson follows her soon after, against May's advice. Hearing of this, Triplett races to disable the explosives, and then searches for the temple to help Skye.
Skye reaches the temple to find Raina waiting for her. The Obelisk floats to a central pedestal, and the temple begins to close itself. Coulson is stopped from entering by Mack, but Triplett manages to get in before the room is sealed. The Obelisk opens, revealing crystals inside that release a burst of mist. Skye and Raina begin to be covered by cocoons, and in an attempt to save them, Triplett smashes the Obelisk and the crystals. This doesn't work, and the two become fully encased. Triplett, in despair at having lost his friend Skye, is turned to stone by a shard of the Obelisk. Raina's cocoon begins to crack, her appearance having been transformed during the process. Skye triumphantly erupts out of her own cocoon, her new earthquake abilities shaking the entire island, but this changes to guilt and horror as she watches Triplett's petrified body crumble in front of her.
In an end tag, another Obelisk tells a man with no eyes that "there's someone new". He calls another person to say that he is "on it".