We jump back to the day S.H.I.E.L.D. fell. The world is in chaos. A team of Hydra agents hold Mack and a few others at gunpoint in a room on an aircraft carrier. They shoot one agent. Another is about to be executed when Bobbi storms into the room. She takes out the bad guys one by one. She gets a last-minute assist from Isabelle “Izzy” Hartley. They have a plan. They have orders to save S.H.I.E.L.D.
Bobbi and Hartley find an injured Commander Robert Gonzales. Mack helps set his leg. They need to move. Before they do, Bobbi gives Hartley a keychain that reads Franny’s Saloon. She wants her to give it to Hunter. Bobbi won’t be able to do it herself. She has orders to sink the ship they in what’s sure to be a suicide mission. Mack won’t let her do it alone. Gonzales agrees that they will all finish this mission together.
In the present day, after Bobbi returns with her story of Hunter’s disappearance, she sneaks into a server room to fiddle with the equipment. Elsewhere, Coulson confronts Mack about his double agent ways. He realizes he’s in cahoots with Bobbi, who has retrieved the toolbox Director Fury had provided in “Beginning of the End.” May confronts her. A mighty fight takes place. Bobbi ends up shutting down all power. This allows for her to escape. The toolbox is gone, too.
In her secret cabin, Skye tries on the gloves Simmons made for her. She finds that the paneling on the wall hides a metal wall that features a Hulk-like fist mark. Moments later, there’s a knock on the door. It’s Gordon, the man with no eyes. He explains how the mist changes everyone in different ways. He wants to take her to a place where she can be with people like them. Gordon will return when she’s ready.
At headquarters, Simmons uses her ingenuity to neutralize Bobbi. May finds a gas mask. She realizes that Bobbi and Mack aren’t looking to escape. Others are coming to join them. Gas fills every room at headquarters. Mack knows what’s coming. He saves Fitz as a blast that nearly decapitates him. Gonzales, Calderon, Weaver and other agents enter the area. They learn that Skye is being held at “the retreat.” Bobbi wants to be on the team that goes after her.
At the cabin, Skye discovers that she has the power to make flowing water move into some form of suspended animation. She gets a call from May. Skye needs to get out of there pronto. Moments later, Bobbi and her team arrive. Skye is on the run. Bobbi tells the other agents they are to use icers only. Then we jump back to the day S.H.I.E.L.D. fell. Bobbi is ordered by Gonzales to sink the carrier. However, she’s swayed by Mack, Hartley and others to take back the ship, and that’s just what they do.
In the present day, Gonzales admits that he was wrong in wanting to sink the aircraft carrier. He wants Coulson to open the toolbox. He doesn’t want secrets to bring down S.H.I.E.L.D. again. Gonzales believes Coulson’s team will eventually see things his way. That’s not going to happen today though. May ices Gonzales and several other agents. She frees Coulson from his bindings. She sends him off to find Skye. May then surrenders to Agent Weaver.
At the retreat, Skye races through the woods. She gets into a violent fight with a pursuing agent. Calderon and Bobbi arrive on the scene. Skye is cornered. Calderon fires his gun. Skye instinctively holds up her hands to defend herself. She ends up creating a wave of seismic energy. A tree is obliterated. A large chard of wood hits Calderon in the chest. Skye is horrified by what she’s done. She calls for help from Gordon, who appears to take her away through a portal. Bobbi is left behind surveying the destruction as tears well up in her eyes.
On a Florida beach bar, Coulson plays with one of the umbrellas in his colorful cocktail. Hunter takes a seat beside him. The two men exchange pleasantries. Hunter signs his name on a napkin. It’s his way of accepting the full time position Coulson had offered him a while back. Coulson can’t help but let out a little smile. Looks like this unlikely duo will be working together on a new plan.