Plus, the long-simmering romantic tension between Root and Shaw will finally become an actual relationship. So the world may be ending, and Samaritan may control the government, but at least we’ll get to see the greatest love story ever told about a hacker and a ninja.
—  Ars Technica providing us with the single greatest line for Root/Shaw ever: “The greatest love story ever told about a hacker and a ninja.”
  • Studio Executives: Nathan, can we talk to you for a second?
  • Nathan Fillion: Yes, what is it?
  • Studio: We need to put and end to the constant jokes about Firefly. We get it! You loved working on that show, and you're upset it got cancelled. But seriously, you've made a blatant reference to it in every single thing you're in. Castle, Percy Jackson, that thing with Neil Patrick Harris and the puppets, where does it end?
  • Nathan: Well, alright. I suppose you deserve a little peace of mind. A little...Serenity.
  • Nathan: Why, it's pretty cunning, don'tcha think?
  • Studio: NO! STOP!
  • Nathan: I aim to misbehave.
  • Nathan: This wouldn't be an issue if it weren't for your sudden but inevitable betrayal.

Eventually, Shaw will have to go back to the subway, especially with the Machine operational again, and drive the train car back into the subway and seal it (she and Fusco will spend a lot of time doing that, Shaw will feed him donuts as a joke, but they actually get into it).

But she doesn’t really stay in the Subway anymore, after the simulations its not a place Shaw can really find refuge in, but that’s okay, in Harold’s absence Shaw also gets a part of Harold’s (and Root’s) vast wealth and properties– and among them are different abandoned libraries Harold apparently owned.

Shaw is starting from scratch but she’s not going to repeat the same mistakes, she’s going to improve on the system, especially since there are some teams running around. She’s going to keep tabs on them but not really interfere until the Machine will say its absolutely necessary.

Shaw will also rebuild her networks and first order of business, she meets up with Zoe Morgan. Zoe is beyond shocked to see Shaw but happy all the same, Zoe doesn’t ask about John and Harold the outage, the missile in the middle of New York, the virus. Zoe knows when her city was under siege.

Shaw clues Zoe into the existence of the Machine and Zoe isn’t actually that shocked to know this.

Fusco points Shaw to an upcoming detective in the force, Dani Silva, Shaw only met her briefly but something about Silva reminds her of Carter and that’s always a good thing.

Shaw decides not to stick to any kind of uniform, that’s what gets things like ‘Man in the Suit’ in people’s radar in the first place. 

There’s also a lot of clean-up that needs to be done– Harold’s virus burned down the world, and that wasn’t without consequence. Shaw also does a little bit of Samaritan clean-up too, without a leader the Samaritan cells broke-up into smaller fractious groups, trying to bring about their own plans.

Shaw goes to Johannesburg and shuts down a prison, she only sticks around long enough to watch Samuel walk out of the prison.

She is not at all surprised to find Control in a dark cell.

“Agent Shaw,” Control said, in her usual way, like Shaw just walked in her office to be reprimanded, and not like she was rescuing her.

“Ma’am,” she returned, even. 

“You’re hard to kill,” Shaw might be mistaken but Control sounded a little too proud there.

“Likewise,” Shaw tipped her head, “Wanna get out of here or do you want to continue bantering?”

They made it out alive, Shaw briefed her on what’s been going on in the world, about how the Northern Lights program’s been shut down and how Samaritan allowed a presidential assassination to take place.

“Your daughter’s alright,” Shaw said, after a beat, repeating the Machine’s words.

The tightness in Control’s features relaxed.

Shaw dropped Control off in an Airforce base, and Shaw made her own way out.

A private jet. Money had its perks. 

There’s some things to get used to too, Shaw has a serious conversation with the Machine about boundaries. 

Shaw returns home and picks up Bear from Lionel. 

Lee fussed over Bear before handing him over to Shaw.

“You okay?” Lionel asked.

Bear moved to her and she caught his leash, the Machine spoke at the same time, “Honey, you ready?”

A corner of Shaw’s mouth quirked up, “Absolutely.”