The episode kicks off with Helen treating Emily to brunch as she explains that she needs her mind to make her better and stronger than Piper.
Emily plays coy, but attempts to slash Helen's throat only to realize that she's also AI and indestructable.
Helen tells her she's failed the test and will test her code out on Justin.
Jo worries when she cannot reach Brooks and asks Chris to do some digging.
He sends over some friends to do a wellness check on his apartment after he finds out that Emily never made it back to the hospital but finds out it's being swarmed by FBI agents.
Jo gets a call from the hospital that an injured Brooks was dropped off last night.
Jo helps him escape from the hospital since the FBI is after him. Brooks cannot remember who saved him and drove him to the hospital, but he believes it was Helen.
Benny, who is in custody, informs him that it's impossible. But Jo doesn't take Benny's word for it because he's unable to tell her what Helen's true plan in.
He mentions that they're all programmed to live a life and gather/collect data until the upload begins, which will shut them down.
The FBI comes looking for Brooks at the precinct and though Jo wants to help him escape, he tells her he has to turn himself in. Before he does, they kiss in an intense moment.
As Brooks is being investigated, a Department of Justice employee comes in and clears the room.
Then, they clear all charges against him and reinstate him as part of the FBI.
Brooks is suspicious and throws out his new cell phone, keys, and badge upon leaving the workplace.
He arrives at Jo's place and tells her that he's being followed. The two devise a plan to catch the person following him and also make out a little more.
The plan goes off without a hitch, but they're surprised to see it's Helen following them.
Except it isn't really Helen but her creator Loretta, who also works for the FBI and promises to give them a weapon to kill Helen in exchange for the exabyte disc that Jo possesses.
They refuse, but when the upload begins and Benny and Piper begin floating in the air, she agrees.
The upload is thwarted, which gives Jo enough time to get to Plum Island with Brooks, get the weapon in exchange for a fake disc, and try to stop Helen.
But Helen's so powerful, they don't stand a chance.
Meanwhile, Piper convinces Alex to take her to free Benny so that they can save Jo. She believes Jo won't make it out alive otherwise.
Emily betrays Justin, the AI who devised a plan for them to run away before Helen can kill them.
Emily coded into his psyche so well that he didn't even realize he was in a simulation.
Helen killed him for her own benefit.