The episode opens with the Oliver laying on the floor in the Arrowcave, temporarily stunned from the explosion at the end of the last episode. After checking on Felicity, he grabs a gun and tries to find Chase, who set the explosion off. It turns out that Chase used an EMP to fry every circuit in the Arrowcave...including the implant that helps Felicity walk.
It turns out that Chase's plan was to trap Oliver and Felicity in the Arrowcave, which was his plan all along. He even welded shut the emergency exit, to ensure that Oliver dies a slow death inside his lair.
In a flashback to 11 months, Felicity and Oliver argue over whether they should expand the team and share some mild flirting while looking for a new crime lord in Star City.
In the present day, Quentin is dealing with his own crisis: every defense attorney in the city is petitioning to overturn all of Chase's convictions because he's a serial killer. Rene sends Curtis to check the bunker for Oliver or Felicity, since he can't get a hold of either of them. Curtis discovers that the Arrowcave is shut down, although he does hear some explosions from Oliver trying to blast the door of the bunker down.
Oliver figures out that Chase is going after William (Oliver's on) and tells Felicity that Chase knows about William's existence. Felicity immediately tells Oliver to look at Cisco's original plans for a way out.
Back at the Diggle household, Lyla and Diggle argue over whose morality is more compromised. They get interrupted by Rene, Dinah, and Curtis, who tell the Diggles about the Bunker going down.
Oliver decides to climb up the elevator shaft, even though Felicity points out that Chase probably booby trapped it. Oliver tries to do it anyways, sets off a booby trap and ends up with a rivet in his back for his troubles.
Felicity stitches Oliver up and lectures him for not trusting her, including with Felix. Oliver admits that Felicity was right and tells her to figure out a plan and he'll support it.
The rest of the team pieces together that Oliver and Felicity are trapped in the bunker, and Curtis predicts they only have a few hours of air left.
Meanwhile, Felicity suggests they use Oliver's old motorcycle to generate enough electricity to power up a cellular link in the mainframe, so they can get a message out.
In a flashback, Curtis points out that Felicity and Oliver are flirting like crazy again, but Felicity says that Oliver still doesn't trust her. Curtis says they should try to work it out and reveals that he set up an impromptu date between the pair that evening.
Rene and Curtis rappel onto the roof of the bunker so they can try to weld through it. Meanwhile, Dinah tries to get Diggle to open up about his relationship problems, and says that her relationship with her undercover partner occasionally needed to keep things from each other for their own sanity.
Back in the Arrowcave, Oliver says that he only didn't back Felicity's play not because he doesn't trust her, but because he didn't want her to end up like him. However, their conversation gets cut off when the mainframe turns on and promptly explodes, causing a methane gas pipe to rupture.
Oliver tries patching the pipe with duct tape, but it pops. Felicity they have a matter of minutes before they suffocate, but Oliver realizes they can escape via a steam pipe under the bunker. However, they'll need to break open a steel door...which might be difficult given all the methane in the air.
Rene and Curtis tries to melt the roof of the bunker, but they cause an explosion from all the methane.
Felicity rigs one of Oliver's arrows with explosives, and Oliver shoots a bullseye to blow the door open. They discover it's a two story drop to get into the steam pipe.
In a flashback, Oliver and Felicity get drunk and goof around with the salmon ladder and make out for a bit before they start stripping and getting busy in the bunker.
Lyla brings Curtis one of his T-Spheres, as ARGUS keeps tabs on interesting tech. Diggle is upset, but Lyla thinks they can use the T-Sphere to bust Oliver out of the bunker.
Oliver and Felicity find out the steam pipe is a dead end and Oliver passes out from blood loss, methane inhalation and carrying Felicity on his back for a while. Felicity wakes Oliver up, and Oliver admits to Felicity that he enjoys killing people and that's why he didn't want Felicity to turn out like him. Oliver then passes out...for real this time.
In another flashback, Oliver and Felicity have some pillowtalk, but Felicity tells Oliver that she's not getting back together with him. She admits that she just can't get past that, even though she loves him.
In the present day, Lyla gives Diggle a list of every black op she's signed off on, but says that she deserves Diggle's trust...just as Diggle trusts Oliver despite all of his morally compromised decisions. Diggle doesn't have a retort for that (because SHE'S RIGHT) but Curtis interrupts saying he's figured out how to rescue Oliver and Felicity.
Oliver wakes up again, and Felicity tells Oliver that Adrian Chase is wrong about him. After all, Oliver endured 5 years of hell and 5 years of self-inflicted vigilantism facing the worst criminals Star City has to offer, and he still hasn't turned into a monster. So, Felicity suggests that maybe Chase's torture just got into Oliver's head and that he's not actually the unrepentant sociopath that Oliver thinks he is.
Just then, Curtis's T-Sphere blows a hole in the wall, saving them. Unfortunately, Curtis reveals they have another problem: the mainframe is set to turn back on, which will cause all the methane to explode and cause a massive explosion. However, Curtis has a plan to get the vents back online before the mainframe comes back on: manually turning the vents on while Team Arrow retrieves Oliver and Felicity. Things get a little hairy when Oliver passes out and Diggle realizes they don't have enough rope to climb down to the bunker, but a T-Sphere loaded with adrenaline and Oliver's insane upper body strength ends up saving the day.
Lyla offers up ARGUS as a temporary base, and Diggle apologizes to Lyla for not trusting her. Meanwhile, Oliver gets out of emergency surgery and asks to see Felicity.
In a final flashback, Felicity apologizes to walking out on Oliver and admits that she's not ready to give them another chance, but doesn't shut the door on a future relationship. Oliver promises that he's not going anywhere.
In the present day, Oliver thanks Felicity for giving him a pep talk about his character. Felicity then apologizes for joining up with Helix and says she understands why he lied about William. Felicity then tells Oliver that he should figure out what sort of person he is.
The episode ends with Chase finding William as he gets off the school bus.