May makes some fancy evasive maneuvers as attacking QuinJets get missile lock on the bus. She manages to dive and cloak as explosions fill the sky. The Hydra pilots believe they have hit their intended target. The bus is safely hidden and headed for San Juan. May breaks the news to Coulson that Hydra has Skye.
Bobbi asks Hunter to join him to meet with her San Juan contact, Diego. She’s hiding a thumb drive from him, or so she thought. Hunter is hip to her secret stash, but will give her the backup she needs regardless. They get a signal from Diego as he meets with some Hydra agents. Bobbi is given a piece of paper with an address. Time to investigate.
Ward called an audible when he brought Skye back with him. His orders were to only collect Raina. He introduces her to her father. The Doctor introduces himself. She only knows him as a monster and a murderer. The Doctor explains that he wasn’t always like he is now. He apologizes for not being there for her in the past. He lets Skye know that she isn’t going anywhere. This is her destiny.
The Doctor tells Skye that her mother comes from a line of people who have a gift. She was murdered by men who said she was dangerous. He tells her how Whitehall butchered her mom’s body and ultimately threw her in a ditch like she was garbage. Their conversation is interrupted when The Doctor is summoned away. He’s to meet with Whitehall, who realizes Skye is his daughter. He orders her to hold the Obelisk. Two Hydra agents go down in a fight, but Whitehall and his minions ultimately get the upper hand on Skye, Ward and The Doctor.
Hydra is attempting to drill into the chamber that leads to the Ancient City. They can’t be allowed to enter with the obelisk. Trip and Agent Koenig will have to make use of some explosives from 1945 that can’t be triggered remotely. There’s a slim chance that Mack may still be alive. That means there’s hope he can be saved. Teams of S.H.I.E.L.D. agents set off on separate missions to thwart Hydra’s plans.
The Doctor manages to escape. He leaves Skye and Ward behind so he can deal with Whitehall, who draws a gun on him. BANG! BANG! Coulson shoots Whitehall dead from behind. The Doctor is outraged. His chance for vengeance is gone. Various battles take place in various locations above the Ancient City. Skye shoots Ward after he helps her escape. She then threatens to shoot her father to get him to stop pummeling Coulson. She orders The Doctor to leave. He reveals that Skye’s real name is Daisy before walking away. Elsewhere, Ward convinces a disillusioned Agent 33 to help him.
While tending to a wounded Coulson, Skye vows to make things right. She goes after the Obelisk, but Raina is already in possession of it. She asks a still-living Mack (who is not really Mack) to take her to the temple. Up above, Coulson realizes that Skye went after Raina. He goes after her. Trip races to neutralize the explosives once he realizes that his team is in danger.
Raina reaches a chamber with a pedestal in its center. Skye runs into a catatonic Mack. She promises to come back for him. She tracks down Raina, who wants to find out what they will become. The Obelisk floats and lands on the pedestal. Coulson manages to get past Mack. He can’t get inside the closing chamber, but Trip does. The Obelisk changes shape. A shockwave of white mist envelopes the room.
Mack collapses outside the chamber. Inside, to their horror, Raina and Skye begin to petrify. Trip is remarkably unaffected. He knows he has to save Skye. He has to save the world from this deadly weapon. He kicks it off the pedestal. The Obelisk is knocked out of its orbital spin as pieces explode. Trip is horrified to see that Skye and Raina are completely petrified. He notices that shards of the Obelisk have hit his body. Horror engulfs Trip’s face as he crusts over into full volcanic petrification.
Raina’s shell starts to crack. She looks different, as if her arm is covered in thorns. She has unnaturally small pupils in her eyes. Skye’s shell also cracks. Physically, she looks the same. Skye sees what’s happened to Trip. Guilt and horror engulf her face. Her arm shakes. As her volcanic chrysalis explodes off, everything shakes. It’s an earthquake. The rest of the team fears the worst in their various locations. Falling rubble allows for only a glimpse of Raina. The descending debris hits Trip as he cracks apart. Skye is horrified as she sees her friend’s crumbled remains. Rubble continues to fall.
In an office filled with books and scientific papers, an unidentified man pulls a glowing Obelisk from a case. He’s unharmed after touching it. This mystery figure makes a call. He lets the person on the other end of the line know that there’s someone new. He says that the others should be informed that he’s “on it.” When the man’s face is finally revealed, he is shown as having no eyes. The area where they should be is completely smooth.