The episode opens with Coulson on a car lot, carrying a metal briefcase in his hand. The salesman starts his routine, saying he has a super power that lets him tell any man what kind of car he should be driving. Coulson is not impressed. They begin to discuss Coulson buying an SUV when Hunter drives up in a Jeep off the lot, telling Coulson to get in. Coulson and Hunter argue over stealing the Jeep. When the salesman threatens to call the police, Coulson I.C.E.s him. Coulson and Hunter drive off in the Jeep.
Skye wakes up on a table. Gordon and Lincoln are performing some kind of acupuncture-like process on Skye. Gordon leaves Skye with Lincoln, Skye’s transitioner. He explains that everyone who goes through terrigenesis has a transitioner, and describes the evolutionary process of terrigenesis and how he’s trying to help it along. Skye is worried about her friends, but Lincoln reminds her that she’s being hunted.
Back at S.H.I.E.L.D. HQ, Morse and Gonzales are discussing the failed attempt to capture Skye. Morse defends Skye, saying that Calderon pulled a gun on her and that she’s still an S.H.I.E.L.D. agent, but Gonzales still says she was armed and hostile and is unsympathetic. Morse says Coulson is as in the dark as anyone else, but Gonzales questions that assumption, saying they need to get into the Toolbox.
FitzSimmons examining that very problem, but no progress seems to be being made. Gonzales tells them that he wanted to recruit them out of the academy, but Coulson sept them out from under him. Gonzales tries to smooth things over and get them on his side, but FitzSimmons are still cold and apprehensive. Morse says they’re not prisoners and are free to go as soon as they’re debriefed. Fitz immediately leaves to pack his things.
Coulson and Hunter arrive at the cabin safe house and find the damage left behind by S.H.I.E.L.D.’s encounter with Skye. They find video footage of Skye’s powers at work and Gordon taking Skye away.
Lincoln walks in on Skye, who has finished getting dressed. She says she feels normal. She wants to get a message to her friends, but Lincoln says Gordon is the only one who can contact the outside world. Skye asks were they are, and he says the name is Chinese, Li Shi, but they just call it Afterlife.
Lincoln says he doesn’t know if they’re actually in China, only Gordon knows. Skye says it sounds like a prison. Lincoln says nobody lives here permanently, it’s more like a waystation, someplace people go to transition or when they need a safe place to hide out. Skye asks why so many people are staring at her. Lincoln explains that everyone here is a descendent, but they’re here to be evaluated. Only a few people get chosen for terrigenesis a year. Skye “jumped the line,” and is the first to go through terrigenesis with a Diviner at a Kree temple in thousands of years. The others are envious, which Skye doesn’t understand. Skye asks about Raina and Cal, but Lincoln says there’s no one here who will harm her.
Gonzales is trying to question May, but she’s giving him the silent treatment. Gonzales asks if May is loyal to Coulson or S.H.I.E.L.D., and May says they’re the same. Gonzales tells her about the encounter with Skye, and May defends Coulson’s decisions.
Morse watches the interrogation on a tablet. Mack finds her and asks why she’s hanging out alone. She says there’s too much bad blood, too many agents see them as traitors. Morse says that Coulson is a good man, but Mack says he’s a good man who has been compromised.
Gonzales says that Skye and Coulson should both be put on the Index. He reminds May that sometimes people with powers lose control. He shows her the file on Bahrain, and says she had to put someone with powers down, earning her the nickname the Cavalry. Gonzales says he wants to avoid having to put Coulson and Skye down, and that he wants her to help him find them to avoid a deadly showdown. May says when he’s ready, Coulson will find Gonzales.
Coulson and Hunter share a drink at the cabin. Hunter voices his anger over Bobbi and Mack’s betrayal. Coulson defends them as good agents. Hunter says there are few people he’d fight for but Coulson is one of them, but he wouldn’t fight for Gonzales if hell froze over. Coulson defends Gonzales as a good guy, and questions his own position as director. Coulson says there are no good options. Hunter says it may be time for the bad ones.
Morse approaches Simmons. She says Fitz is cleared to go, and asks if Simmons is leaving as well. Simmons says she wants this to blow over and get back to normal. Morse says that’ll happen when the Toolbox is open. Simmons says they’re looking at it wrong. It’s not a tech solution, but a lab solution.
Lincoln brings Skye to her room at Afterlife. Lincoln says Skye’s gloves compromised her transition process. Lincoln tells her she’s not strictly human any longer. Skye says she want to get rid of her powers. Lincoln says it’s irreversible.
Hunter is asleep on the couch and is awoken by the sound of an incoming aircraft. Coulson says he invited the other S.H.I.E.L.D. Coulson plans to steal the Quinjet they brought with them. He says he has reinforcements on the way. Coulson tells Hunter to stick to non-lethal weapons, and they hole up in the cabin.
Gonzales fills Morse in on what’s going on with Coulson.
At Afterlife, Lincoln shows Skye around. They pass a transition room that Lincoln says they don’t use anymore. They find an open area where Lincoln invites Skye to show him her powers. Lincoln takes Skye’s hand and show her his gift, to generate and manipulate electric charges. He says it took a while to get control, and that he almost burned Afterlife down. He uses electricity to levitate Skye into the air.
Fitz is packing up his stuff. Mack finds him and says he hates to see him leave. Fitz doesn’t warm up to him. Mack says he doesn’t want Fitz to leave, that he’s still Fitz’s friend. He tells Fitz that Simmons found a way into the box. Fitz doesn’t understand why she’d do what she’s doing, but then seems to have an idea.
The S.H.I.E.L.D. agents continue to try to break into the cabin. Coulson tells Hunter there’s only one reinforcement on the way. He opens the suitcase. It’s a 21st century Howling Commando kit. Coulson pulls out a deck of cards and uses it to set up a hologram image of the two of them. The soldiers fall for it and Coulson I.C.E.s them.
Lincoln and Skye run into Gordon. Gordon says he has pressing matters to look into. Skye asks to send a message to her friends. Gordon says he needs to ask permission, but that they’ll advise against it. She asks about Raina and Cal, but Gordon says he can’t divulge their location. Skye asks who Gordon needs permission from. Lincoln says the elders, who are afraid Skye has given away their secret.
Gordon teleports to the place where he’s keeping Cal. Cal is angry, but Gordon says he’s lucky they kept him alive. Cal suspects that they’ve found Skye and that she’s here. Cal wants to see Daisy, but Gordon refuses and they fight. Gordon uses his powers to get the better of Cal. Gordon says Cal’s lack of self-control has threatened their safety and sealed Cal’s own fate as well as Skye’s.
Coulson and Hunter dress up as the soldiers and head out of the cabin. They approach the Quinjet, but are immediately recognized. They find themselves surrounded by another cloaked Quinjet.
Simmons is working on the Toolbox when Morse checks in. Fitz shows up and is upset. Fitz picks up the Toolbox and an agent pulls a gun on him. Fitz says he thinks Simmons wants him to leave. Simmons says she thinks it’s best if he does.
Coulson and Hunter are being loaded up as prisoners on the Quinjet. The hangar door is closing when it is suddenly stopped and is pulled open by Deathlok. Deathlok takes out several guards and grounds the other Quinjet. Coulson introduces Hunter to Mike Petersen, who’s gotten some nice upgrades. Deathlok gets ready to get the Quinjet in the air.
Gonzales tells Morse that Hunter and Deathlok are working with Coulson. He tells Morse to bring him the Bus and Agent May.
Lincoln and Skye are enjoying some popcorn. Lincoln again asks Skye to show him her powers, says they’ll give her a guide to help her master them. He says that Skye’s powers are easy compared to the other one’s, and Skye realizes that he’s talking about Raina and that she’s here. They argue, and Skye begins to shake the room. Skye storms out and opens the other transition room they walked by before. Raina is there and miserable, hiding from the light of day. Raina shows herself to Skye, says she is on the outside was Skye is on the inside. Skye uses her powers on Raina until Skye’s mother, Jiaying, shows up behind her.
Jiaying reminds everyone that they’re all guests in her house, and that Raina deserves the same care as anyone else. She says both Skye and Raina are “one of us.” Skye says she can’t stay if Raina is here. Jiaying says the choice is Raina’s, but that she has chosen to be Skye’s guide if she stays. She says if, after a few days, they don’t’ feel a connection, then they never have to see each other again.
Gordon returns to Cal, this time with Jiaying. Cal says he told Jiaying he would find Daisy. Jiaying thanks him. He asks to see Daisy. Jiaying says no.
Gonzales returns to the Iliad with May. He brings a gun that his father used in World War II and gives it to May, tell her to shoot him if she really thinks he’s a traitor. Gonzales offers May a seat on his board, saying that when they catch Coulson he should have a strong advocate on the board. May picks up the gun and passes it back to Gonzales. Gonzales monologues over a scene of Fitz leaving. He asks May to help defend S.H.I.E.L.D.
Coulson’s Quinjet is in the air. Deathlok has been tracking Doctor List. List has been looking for powered people to experiment on. Coulson says he doesn’t think Gordon is involved with List, but that Gordon is connected to Skye’s father and the powered people he knows about. Coulson says there’s only one man who is connected to both these powered people and Hydra. If they’re going to find Skye, they need to find Grant Ward.
Simmons tells Mack and Morse that she’s done everything she can, but without Coulson she simply can’t open the Toolbox. Fitz hails a cab and pulls the actual Toolbox out of his bag.