In a flashback to the day S.H.I.E.L.D. fell to Hydra (remember that from Captain America: Winter Soldier?), Mack and his team are being held hostage. The lead Hydra guy shoots one of his team when Mack doesn’t speak up as the lead engineer, and just as he’s about to kill another person, Bobbi storms in like a badass cavalry with Izzy Hartley (Lucy Lawless!!!) and takes out the Hydra agents. They say that Nick Fury left them orders to save S.H.I.E.L.D. and they’re being excellent soldiers.
Back in the present, Bobbi arrives back at headquarters and begins some sabotage as Coulson finally allows Mack to work on Lola – under supervision, naturally. Bobbi approaches and apologizes for her relationship with Hunter and how it has affected S.H.I.E.L.D. and Coulson’s like, “It’s cool. I’ve got some feelers out looking for him and we’ll see if he wants to be here or not.” Then Bobbi creeps around some corridors until she finds a mainframe then inserts a flash drive, presumably to monitor Coulson for the real S.H.I.E.L.D.
Skye and Simmons video chat as Skye adjusts to a life of solitude and seclusion. Simmons says May will be visiting her soon, and that Skye should try on the super special gloves Simmons made for her. They’re laced with a microthread that will accelerate Skye’s healing and minimize the damage her power does to her. Fitz is cheesed off at Simmons, calling her gloves a “science experiment.”
Coulson tells Mack that he knows he put some component into Lola without Coulson’s knowledge and he might as well come clean. At the same time, Bobbi is lasering a big hole into Coulson’s desk to recover Nick Fury’s toolbox (because Coulson will never notice this!). Coulson gives Mack a chance to be brutally honest and declare his true allegiance, and Mack insists he works for S.H.I.E.L.D., so all of the innocuous mechanics in the background pull their guns on Mack. (Why didn’t he use the same verbiage he employed with Hunter?) Coulson asks who else is in on this plot with Mack, decides Hunter must have been a pawn, and then calls May immediately.
May shows up at Coulson’s office to find Bobbi snapping up the toolbox. Bobbi insists that Coulson’s operation isn’t the real S.H.I.E.L.D. and backflips out a window so May gives chase. Bobbie runs down some stairs, May intercepts, and the two let loose on each other as they each grab and lose the toolbox repeatedly. As Bobbi grabs the toolbox and May has her dead to rights, two more agents come in and Bobbi triggers an EMP. All of the power to headquarters dies, allowing her and Mack to make swift escapes. May and Fitz report the details of Bobbi and Mack’s duplicity to Coulson and Fitz decides to head to the control room to initiate a manual lockdown. May is concerned that Bobbi and Mack know the ins and outs of their whole operation and tells Coulson about Bobbi’s declaration that she works for the real S.H.I.E.L.D. and he’s like, “What the hell is that supposed to mean?”
Flashing back to the day S.H.I.E.L.D. fell, Mack, Bobbi, and Izzy search for, and find, Commander Gonzales, who is grievously hurt and ready to shoot anyone who can’t adequately prove their allegiance. They’re there to extract him, but he’s got an ax wound to the thigh and this isn’t going to be so easy. Back in the present, Bobbi makes contact with Gonzales and Agent Calderon for updates. She informs them that she had to go to plan B because she was found out, but she has the toolbox. They tell her they haven’t found sign of Hunter or the pod he escaped in, and there’s no word on Mack yet. They all assume, rightly, that if Coulson knew something was up he would have sent Skye someplace far away.
Skye decides to start a fire and try on her new gloves, and immediately heads to her computer. Suspiciously there’s not connection to her computer anymore, so she calls Simmons about the gloves. There is no answer, so she leaves a message about them making her feel woozy, and discovers false panels on the wall of her cabin. She pulls some of them down and finds a – ahem – hulking fist imprint in a metal wall. Then she begins to hear creepy sounds and curses Fitz for making her watch Paranormal Activity. She grabs a fire poker and has a look around, then hears a knock at the door. With her nervousness apparently evaporated, Skye opens the door and it’s Gordon, who wants to have a word.
Gordon tells Skye that he can see, but not with eyes, of course, and he’s not there to hurt her. He’s like her and has come as a similarly afflicted friend.
Gordon: I wish you wouldn’t stare.
Skye: Uh –
Gordon: That was a joke. I’m not very good at them. I don’t mind that you’re curious, honestly. And yes, I used to have eyes. They were blue. This…this was the obvious change for me. What happens inside can be just as profound. You see, the mist changes everyone differently. The real difference between the two of us is what happened after we went through the mist.
Skye: What do you mean?
Gordon: I knew from an early age how special I was. Had a mentor, a guide of sorts. And the first thing she did after I transformed was embrace me. Tell me, Skye, what was the first thing that S.H.I.E.L.D. did to you?
Bobbi sneaks up on Simmons who is rooting through a locker and glad to see a friendly face. And Fitz is in the control room setting up his override. Coulson tells May that the agents he sent after Mack were found unconscious and Mack disabled the planes. He and May note that they aren’t killing people, behavior not in line with Hydra agents, but they did steal the toolbox and that’s probably not all they were after.
Gordon asks Skye how her power feels to her and she says it feels like a thousand bees inside her, all the time, that she can’t stop, ever. (That’s rough.) He asks why she’d want to stop it, and she’s like, “Dude, I’m out here destroying stuff!” He thinks she’s wrong about that.
Gordon: Every object in this universe gives off a vibration, did you know that? Nothing rests, and you have the ability to tap into those vibrations. You could become magnificent, but something’s inhibiting you, constraining your energy.
Skye: No, my friend’s a scientist. She made these to protect me.
Gordon: Or do they protect people from you?
Skye: No, it’s not like that. My powers, I can’t control them. And when I try to, it hurts me.
Gordon: Most gifts come with a price, but you could learn to manage it.
Gordon tells Skye she doesn’t have the tools to be her truest self without fear or pain yet, but she can if she comes along with him. He is with people “like us” who can help her learn about herself in a safe environment, and when she’s ready he’ll find her and he disappears.
Simmons tells Bobbi that she’s searching for a prototype that was powered off during the EMP blast and so might still be functional. She hands Bobbi a tiny white tube as she searches and prattles on, and Bobbi’s all, “Look, we’re wasting time and maybe we should go find Fitz.” Simmons finds the “prototype” at last and drops another tiny white tube into Bobbi’s hand, resulting in an electric shock that knocks Bobbi out. Then she radios to Coulson and May that she took Bobbi down like a magician.
While setting up the override, Fitz comes across Bobbi’s planted flash drive and Mack creeps up on him. Mack asks Fitz to trust him, insisting he would never hurt him. Flashing back to The Day S.H.I.E.L.D. Fell, Mack and Bobbi help splint Gonzales’ leg and Izzy says they need to move now because Hydra is closing in on all sides. Izzy is going to clear a path to the top deck while Mack, Gonzales, and the remaining S.H.I.E.L.D. agents follow, and Bobbi gives Izzy a medal to give to Hunter. Bobbi tells Mack that Fury gave her a second mission: to insert a chip into the server core to sink the ship. There would be no way for her to survive but there is cargo on board that Hydra can’t be allowed to acquire, and Gonzales wants to come with her to make absolutely sure that doesn’t happen. Everyone agrees that it’s a fool’s errand if she does it solo, so they all plot to help her sink the ship.
In the present, Coulson and Simmons have handcuffed Bobbi to a pipe and recover Fury’s toolbox while May searches through Bobbi’s locker for some indication of her plan. She finds a false panel with a gas mask inside and discovers that they’re not trying to get out, just as Coulson notices smoke pouring in. Mack continues to try to convince Fitz to trust him and then saves Fitz from the wall explosion that would likely have killed him. Gas masks on, Gonzales and his S.H.I.E.L.D. enter headquarters via the blown wall and authorize medical help for Mack and Fitz.
Flashing back once more, Bobbi, Mack and the crew make their way further below to plant the disk. They come upon Izzy who is handling Hydra agents like a boss. She says she came back down because she realized S.H.I.E.L.D. has retaken the top deck and a turret. Mack wonders if they should try to reclaim the ship, but Gonzales says they’re outnumbered so Bobbi agrees to push on.
Back in the present, The Real S.H.I.E.L.D. has taken over headquarters and they realize that Coulson put Skye in The Retreat formerly used by Bruce Banner. They think she must really be dangerous if he would put her there, so they assign a team of tactical agents plus Bobbi to apprehend Skye. When they break, we see May has observed their whole conversation and knows their plan.
At The Retreat, Skye removes her gloves to reveal her bruised hands and arms. She washes them, and as she relaxes she realizes she is unconsciously morphing the stream of water into a spiral that she can control. And Fitz and Simmons are sitting together in the lab as their stations are ransacked. Agent Weaver approaches them and they discuss who does and doesn’t have the right to call their organization S.H.I.E.L.D. Then Weaver asks Simmons to assist her with Mack’s injuries because she values her expertise and Simmons reluctantly complies.
Coulson has been handcuffed and brought to Gonzales who has taken up temporary post in Coulson’s office. Gonzales says he has no plans to move in, but thinks he should introduce himself as Coulson must be at a disadvantage.
Coulson: Oh no, I actually know quite a bit about you, Robert. You started in S.H.I.E.L.D. young, like me, dropped out for a while when your wife passed but then came back with a vengeance. Rose to command the Iliad three years later and, by all accounts, became one of the best commanders S.H.I.E.L.D. ever had. I know this because I spent months searching for you when S.H.I.E.L.D. fell. Because I’d heard you were a good man, because I wanted you on my team.
Gonzales: I wish I could say the same. I wish you were the man you were even two years ago. But by all accounts, you’re not.
Coulson: You didn’t know me then, and you don’t know me now.
Gonzales: I know that Fury brought you back from the dead.
Coulson: Right. I didn’t ask for that, but I’ve come to appreciate the gesture.
Gonzales: And that he filled your veins with alien blood. God knows what that did. Weaver thinks it made you some kind of messenger for an alien race. Can you say with certainty that that’s not true? And we haven’t even begun to discuss your protege, Skye. You two have a lot in common, at least you once did. What happened in the alien city, Phil? You say that you’re the director, so did she drag you down there kicking and screaming, or were you curious?
Coulson: I went to Puerto Rico to destroy the alien city and stop Dr. Whitehall, and that’s what we did.
Gonzales: In part, that’s true. And that’s why I want to give you a chance to be the good man I know you once were. We believe that Fury kept a lot of what he did from the World Council, that he had objects and people of terrifying power hidden across the globe. We want to find them and we want to make sure that they don’t destroy the very world that we fight so hard to keep safe. Show me how to open it.
May makes her way to a helicopter and uses the communications panel to call Skye and warn her that The Real S.H.I.E.L.D. is coming for her. (This would be a good time for Gordon to show up as he is wont to do, no?) The line disconnects and the power goes out, and as Skye leaves the compound she sees helijets hovering above. Inside, Calderon tells the agents not to approach alone and Bobbi reminds them that Skye is S.H.I.E.L.D., so they should only use icers when trying to capture her.
In yet another flashback, Bobbi, Mack, Gonzales, and the rest are taking fire but have made their way to the engine core. Mack doesn’t think they should blow the ship and Izzy agrees, but Bobbi and Gonzales want to stay on mission. Gonzales says she has her orders and this is not a democracy, but she thinks maybe it should be. Bobbi snaps the disc and vows to take back the ship, so the group takes aim and waits for Hydra to burst into the engine core. In the present, Gonzales recognizes that blowing the ship was the wrong decision and he would have killed hundreds of innocent agents.
Coulson: So now you operate as what? Five friendly faces who agree on everything? I don’t see the other four here talking to me, just you.
Gonzales: I have no desire to be the director.
Coulson: You think I did? Fury chose me.
Gonzales: He made you. You’re literally his creation. He thought of himself as some kind of king, made damn sure he had an heir to the throne. Try and remember, Project Insight was Fury’s idea. Secrets are what brought S.H.I.E.L.D. down the first time, and we won’t let that happen again.
Coulson: If you wanted to talk to me, Agent Gonzales, you should have talked to me. You put spies on my team, invaded my base, hurt my people. Fury’s secrets didn’t bring down S.H.I.E.L.D., Hydra did.
Gonzales: I wonder if you really believe that. Guard, give this to Weaver and Fitz-Simmons. It may take some time, but they’ll figure out how to open it.
Coulson: You really think they’re gonna help you?
Gonzales: Everyone on your team is a S.H.I.E.L.D. agent. We’ll let them make their own decisions.
May: I already made mine.
May shoots Gonzales with an icer and helps Coulson escape through a hidden panel in his office. She gives him some supplies and tells him to find Skye ASAP. Then Weaver and more agents arrive and capture her. Meanwhile, Calderon tells Bobbi about the day he saved Weaver and the academy. He says Hydra released an enhanced human and Weaver was trying to protect herself and others from them, but Bobbi insists that’s not Skye. Just then some agent who can’t follow instructions approaches Skye and they engage in some sweet hand-to-hand. She overpowers him and takes his gun as Calderon and Bobbi arrive. Bobbi shouts for Skye to stop but she reacts with her powers first: with a energy burst, she explodes several trees, causing a piece of wood to impale Calderon. Horrified by what she’s done, Skye calls for Gordon, who arrives in a swirl of blue and whisks her away.
In a Hawaiian bar, Coulson has a super fruity drink and is joined by Hunter. Hunter signs his name on a napkin by way of a contract and wants to know what the next play will be.
The Questions: What’s Coulson’s next play? Will Skye run into her dad now that she’s gone with Gordon? And will the rival S.H.I.E.L.D. factions ever learn to play together again?