Claire Mahoney is a former college student turned Samaritan asset following the completion of an intricate puzzle it designed.
A prodigy, Claire achieved a level of respect by defeating three chess computers in three simultaneous matches. However, she fell into a downward spiral when both her parents died in a freak road accident. She wrote their eulogy.
Claire returned to her studies, but her behavior worried her student adviser who thought that she would attempt suicide. During this period, Claire became enamored with an alternate reality game/scavenger hunt which began with a post on an obscure message board, its symbol being a nautilus shell. Obsessive and with little left to live for, she threw herself into the game, hacking into the computer networks of a private military contractor called Silverpool, stealing evidence of a cover-up. (“Nautilus”)
Recruitment by Samaritan
On the run from Silverpool mercenaries, Claire chases the trail of clues across Manhattan. She is followed by Finch but promptly evades him by blaming him for shooting out a windshield.
Claire runs into Finch again and demands the return of a hard drive previously located in her former household. Finch attempts to reach out to her, but Claire is evasive, denying Finch's perception of her situation, and leaves.
Claire encounters Finch at the penultimate site of the scavenger hunt, the roof of 30 Rockefeller Plaza. He tells her that the intelligence behind the scavenger hunt will try to recruit her, but warns her against taking someone else's imposed discipline over trying to make her own. Refusing to listen, she leaves in pursuit of her final clue.
Arriving at the Octagon building (whose elaborate interior is shaped like a nautilus), Claire is directed to a rooftop on which a switch sits, but its wires have been severed. Armed Silverpool agents close in on her, but as a dismayed Claire is about to give up, an unknown sniper kills the men. She finds a phone in a compartment and receives a message from the game's creator, Samaritan, that it will protect her. Samaritan, having used the game to recruit operatives, labels Claire an asset. She is subsequently reported missing (“Nautilus”).
Finch eventually finds a poster with a secret message in it from Claire which says "You Were Right." Finch meets up with Claire who claims that she is running from Samaritan before she is shot through the shoulder. Finch gets her to a morgue where he operates on her, removing the bullet, when she comes to she explains that when she won the game she was recruited into a group that was involved in data theft and murder and she left after she found out she was responsible for the death of an innocent man named Charles Wynn. When Finch explains that she was been working for an AI called Samaritan, she reveals that she got a hard drive with Samaritan's source code in it and encourages Finch to plug it into his laptop so they can attack Samaritan.
Finch tells her that he doesn't believe her and that he thinks if he plugs in the hard drive it will see all the devices his laptop was ever connected to and will track down all those closest to him. Finch explains that recently he lost someone and that he doesn't intend to do that again. But Claire convinces him to stay by saying that if he leaves now, when she's telling the truth, he'll be leaving her behind for Samaritan.
Finch gets distracted by Reese and Fusco's mission to protect Anna Mueller before he can put in the hard drive and eventually they have to leave when a security guard finds them. As they're about to leave Claire accidentally calls him "Harold" even though he didn't tell her his real name. Claire takes Finch's phone and laptop at gun point and tells him she's taking him to "meet Samaritan."
Claire takes Finch to a charter school and tells him she believes Samaritan is trying to save humans, not subjugate them. She shows him all the good Samaritan is doing in improving education, reduce food and water shortages and that Charles Wynn died in a simple car accident. She explains she was supposed to bring him in if he blew her cover, but brought him to the school because she believed he had the capacity to make the right choice and to join Samaritan to help make a difference and change the world for the better. Finch asks what happens if he refuses and four armed Samaritan agents reveal themselves. Finch says that Samaritan's way seems efficient but it was willing to shoot Claire to get what it wanted and asks her how far she thinks it's willing to go to get the children of the school to believe.
Claire, realizing Finch can't be convinced, reluctantly tells the agents to take him away. As they're leaving the agents are shot by Root who tells Claire to say "Hi" to her boss from her, then shoots her in the shoulder and steals her phone.
Finch reveals he placed a tracking beacon on the laptop that Claire took, but before the signal can be tracked the beacon is destroyed by Greer's team. Claire apologizes to Greer, taking responsibility for Finch's escape since she tried to turn him into an asset instead of bringing him in. Greer assures her he understands. Claire also remarks that the sniper shots were supposed to miss and that she could have died out there because she was actually hit. Greer reminds her if she had died it would have been for a good cause (“Q&A”).