Part 2 of the season finale kicks off with Jo and Brooks trapped inside the building at Plum Island.
Helen's powers are growing stronger as she's able to liquify into tiny nanobytes and move through walls, vents, etc.
Brooks and Jo manage to escape into another room where a bug flies in. Brooks kills it but as Joe examines it, it comes to life and crawls under her skin.
He stops it before it reaches her brain and cuts it out with a knife. Great first date.
Piper convinces Alex to help her break Benny out of jail. Chris is hesitant but agrees, and they all make their way to Plum Island to help Jo and Brooks.
They lock themselves in a chemical room previously used to test anthrax as a weapon. It seems safe enough.
Benny steals the killshot and escapes with the hopes of killing Helen.
Jo tries to talk him out of it, but he's the only one that can get close enough.
During his chat with Helen, he stabs her in the back, but she's not affected as she's grown too powerful.
She kills Benny. As he lays there dying, Jo holds his hand and forgives him.
Meanwhile, Helen transforms into Jo and asks to chat with Brooks and Alex. She tells them Benny's dead and asks for the power source, which tips Alex off.
He realizes it isn't Jo, but it's too late. Helen turns into little nanobytes and swarms them stealing the power source before Piper saves them.
Piper and Jo concoct a plan to ambush Helen when she's not looking. Jo puts the power-inhibiting bracelet on her and punches her killing Helen.
However, on her way down, Helen breaks the glowing orb. Alex and Piper both know this means it'll blow up and kill thousands of people.
Before Piper sacrifices herself, she gives Jo the exabyte she stole from her office.
She then forms a bubble around the orb and explodes with it.
Jo cries, but Alex has an idea. He suggests putting the disk inside Helen since she's just a shell.
To everyone's surprise, it works and Piper is reunited with her family.
Back at the house, DOJ agent Michael comes with a search warrant to find the real exabyte disk since Jo handed Loretta a fake one.
He searches the whole house eventually drilling open a safe with an envelope labeled 'keep safe' that Ed brought home from the precinct.
He opens it to find Piper's necklace inside.
After the whole ordeal, everyone spends time together at home.
Brooks informs Jo that he's into her and asks her to let him know when she's figured her relationship with Alex out.
Alex informs Jo he accepted the position out of town and will be leaving. She asks him to stay, but isn't sure if she wants to start a relationship again.
Loretta and Michael are cleaning up the mess at Plum Island when she reveals that Helen is still online in a different body. The killshot was a serum that gave them the ability to control AI.
They order Piper to open her eyes and she does.