A young boy teleports around an empty room in the year 1983. He has no eyes. Skye’s mother enters and watches. An older man tells her it has been 14 hours since the boy experiences terrigenesis. Skye’s mother, Jiaying, reaches out to him. It takes an effort, but she eventually takes the boy, Gordon, in her arms.
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The older man says they prepared Gordon for this for his entire life, but he still has trouble handling it. Jiaying has apparently been counseling people like Gordon for a long time, because she ages slowly, but she says she won’t live forever.
Cut to Skye sitting on a hospital bed in a S.H.I.E.L.D. facility, quarantined in a transparent room..
Skye wakes up after dreaming of Trip’s death. Coulson is there, sitting outside the quarantine, and she talks about her guilt over Trip. They’re underground, and Coulson says they are all dealing with the loss of Trip in their own way. We see May punching a bag, Fitz and Mack working in the garage, and Bobbi looking at an old photo of her and Trip together. Mack seems to have recovered from whatever took him over in the alien city. Simmons is still there with a team, trying to study and retrieve what they can. Coulson says the Obelisk triggered an earthquake that brought the temple down, and that it’s a miracle Skye is alive. Skye blames herself for what happened, saying that if they she didn’t go down they wouldn’t have failed. Coulson insists they did not fail, that Trip prevented a disaster and that they’ve cut off a head by killing Whitehall.
A small group of men and women sit around a table with Hydra’s insignia. There’s an empty chair for Whitehall. It is apparently a biannual gathering of regional Hydra heads. They question Bakshi’s absence, speculating that his absence is the result of capture or death. Dr, Levy speaks for Baron Von Strucker, and insists that squabbling over who will take over for Whitehall needs to stop. He insists that they continue to underestimate S.H.I.E.L.D. and he wants it to stop. He offers Whitehall’s position to anyone who can eliminate S.H.I.E.L.D. for good. Meanwhile, he’s going to investigate Whitehall’s obsession with ancient artifacts yielded anything usefull.
In the city ruins, someone is ambushed and killed by someone with a spiny hand.
Simmons continues her research. She says she could spend a year investigating, but decides to end it and flood the place. Another researcher is killed. Simmons gets the jump on her and shoots, but the killer escapes.
Bobbi visits Skye in quarantine, with a “survival kit” with a deck of cards, candy bars, travel mix, magazines, and headphones. Bobbi says she’s been in quarantine before and knows it can make someone nuts. Skye says she was starting to feel like a leper, but Bobbi reminds her of how badass she was and calls her a rock star.
Mack asks Ftiz about what he’s working on. Fitz is frustrated with the lack of progress. Mack offers to help. Fitz asks if Mack’s alright, and Mack gets angry. Fitz understands and Mack apologizes once he calms down. Mack asks Fitz to request access to the facility schematics to check ventilation to make sure they’re fully quarantined.
Simmons calls and tells May and Coulson about Raina, the killer in the tunnels. She says Raina was covered in Thorns. Simmons wants to come back to study Raina’s tissue and Skye.
Coulsons calls a team meeting. He’s planning on staging a prisoner exchange with Bakshi as a way to set up a strike against Hydra while they’re week. Mack complains that they’re putting themselves out in the open, and blames Coulson and Skye for being too obsessed with the alien technology that was in their head. The conversation degrades into an argument between all members of the team. Skye’s vitals spike and things around her begin to shake. Coulson finally gets stern and puts an end to the argument.
Coulson finds Bakshi and shows him to General Talbot. Coulson offers Bakshi to Talbot in exchange for backup in dealing with Hydra, and Talbot agrees.
Coulson and May drive with Bakshi in the backseat. May voices concerns about contacting the government when they’re suddenly hit by a truck. Soldiers get out and begin firing at them. They take cover and use marble sized explosive to thin their ranks, and then May takes out the remainder. Coulson pulls Bakshi out of the vehicle, but one last soldier shoots May and Coulson. The soldier orders Bakshi back into the SUV. They drive off and the soldier reveals himself to be Lance Hunter, pretending to be Hydra. May and Coulson are fine, the whole thing was staged.
Fitz and Mack are back in the lab. Fitz is frustrated, saying his heads getting worse.
Bakshi aquires a phone and calls Hydra, setting up a meet. Hunter points a gun at Bakshi, saying he’s being paid to keep him and Whitehall out of the way. Bakshi says if he remains loyal, he’ll be in good with the true heads of Hydra.
Back at the base, Simmons is studying Skye. She tells Skye about Raina, how she was unrecognizable and was altered on a genetic level. Simmons is concerned about an epidemic, and blames herself for the potential outbreak. She says she should have destroyed anything super-powered to begin with instead of studying it. Skye argues, pointing to the Avengers as an example of what good powers can be, but Simmons reminds her that the Avengers wouldn’t be necessary if not for S.H.I.E.L.D. studying aliens. She’s still very upset over Trip.
Cal is sneaking around a dock. Raina finds him. Cal turns and looks at her, revealing her physical transformation, something feline and covered in thorns. She blames Cal, but he says she wanted it. Raina tells him that Daisy was also there when they transformed, and claims she took what was Raina’s. Cal flips Raina over. He’s happy that Daisy changed, but is upset that she likely went back to Coulson. He plans to reconnect with people on the index in order to make trouble for Coulson. Raina wants Cal to fix her, but Cal says there is no fix, that this is what she wanted. Raina is miserable, says her insides feel like gravel and that she cuts herself when she moves. She says she can’t live like this, and Cal tells her not to. They part ways.
Hunter and Bakshi arrive at the home of Mr. Bloom (sp?), where the Hydra meeting had taken place. As Bakshi goes inside, Bobbi joins Hunter in the SUV. Hunter continues to try to find out what Mack and Bobbi are hiding. Bobbi admits they have a secret, that they’re in a support group for people who lived through the Hydra infiltration.
Mack returns the base schematics to Coulson, saying everything is secure. He apologizes for his outburst. Simmons brings up Raina, saying that they should consider breaking protocol and kill Raina on sight, saying this thing may be a contagion. Skye overhears.
Bloom fills in Levy on Hunters apparently being paid by by the Baroness, the Banker, and the Sheik to kill him. Bakshi encourages Bloom to kill Hunter.
Raina looks out into oncoming traffic.
Fitz speaks to Skye about what he’s been studying, saing that her 300 bpm heart rate is “inhuman.” He starts questioning how they found her entirely unharmed, but with destruction all around her. He puts together that Skye was the cause of the earthquake, that Raina wasn’t the only one changed by what happened. Skye begins to freak out and a light shatters behind her. Fitz runs as the power goes out.
Skye tries to hide the broken glass, but May pays her a visit. They start talking about Trip, and we see Coulson visiting what is presumably Trip’s mother. We see Coulson glancing at a picture of the Howling Commandos hanging in her room.
Bloom sets off a protocol signal that alert several individuals near the other Hydra heads. Soldiers surround the SUV and begin firing. Hunter hits a button and guns appear all around the vehicles, firing back. The other Hydra heads are killed, crumbling to dust. Hunter and Bobbi charge in and shoot Bloom. They take Bakshi back, him having been promised to Talbot.
May notices that Skye is bleed. Simmons shows back up. They begin questioning what happened, but Fitz comes back and takes the blame for the mess. Fitz claims that Skye’s DNA is unchanged. May and Simmons clear out, and Fitz lets Skye out of quarantine. Fitz tells Skye he swapped the DNA results, that the actual results are very changed, but that he thinks it should be a secret until everyone, especially Simmons, calms down. Skye cries on Fitz’s shoulder. Fitz comforts her.
Raina walks out into the traffic. The traffic stops around her, and soldiers get out. They say they want to take her in, but she says they’ll either kill her or she’ll make them. A force field appears around her, and Gordon drops down from the sky. He teleports them both away.
In Coulson’s office, a device pops out of the toy Lola that Mack built and begins scanning. Elsewhere, the team trades stories about Trip. In the kitchen, Mack confirms that he’s found Fury’s toolbox in Coulson’s office.
