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The Machine recaps the events of “Nautilus”.

Reese and Finch are at the headquarters of the "Fetch and Retrieve" web development company. They meet the CEO, Lauren Buchanan, and the CTO, Calvin Mazer, both of whom Finch goes with for their presentation of their new search engine algorithm, dubbed "VAL". Reese, meanwhile, spies on their latest number, Anna Mueller, a Fetch & Retrieve employee who immigrated from Munich, Germany at age 14. He watches her leave while she gets a text from someone named Alek, telling her "9PM tonight, don't forget". Reese suspects that she is in an unhealthy relationship.

Finch finds a "lost dog" poster on the streets, embedded with nautilus shells.

Reese is still at Fetch & Retrieve, watching Anna meet with coworker Naresh Prasad. Finch calls to report the reappearance of the nautilus game, and uncovers a hidden message within the poster: "You were right". He realizes he knows who is trying to communicate with him.

That night, Reese follows Anna into a shady-looking building, where "Alek" greets her and lets her in. Reese enters the building and discovers it to be a ring for mixed martial arts - Anna is famous for her skill in the sport and Reese watches her overpower her opponent. He begins to suspect that Anna is a likely perpetrator.

Finch encounters Claire Mahoney on the streets, who looks distraught. She suddenly gets shot by a sniper.

Reese lays out the suspects in the case and researches Anna's background, while Finch keeps an unconscious Claire in a mortuary where he loops a security feed to throw off the guards.

The following morning, Reese visits Anna's household and finds her sister Jill undergoing chemotherapy. Samaritan, meanwhile, is unable to locate Claire.

Claire awakens, explaining her story to Finch - she was recruited by Decima and was employed to perform cybercrimes, though after she hacked into their systems, she uncovered the horrific repercussions of her actions, including the poisoning of Charles Winn. Wanting to escape such a life, she came in search for Finch.

Reese is back at Fetch & Retrieve, where Anna is reprimanded by Buchanan for supposedly invading the privacy of Paul Zimmerman. Reese looks through Anna's computer and finds a transcript of Zimmerman requesting anti-depressants. He abruptly leaves when Anna returns to her workspace.

Finch vaguely explains Decima's motives to Claire and confirms Samaritan's existence - she responds by pulling out a hard drive in which she has stolen source code from the program. She expresses her willingness to work with Finch against Decima.

On the streets, a group of thugs attempt to capture Anna, but Reese saves her. She is brought to the NYPD, where Reese and Fusco interrogate her. Anna presents them with her discovery: when she asks VAL about anti-depressants, it yields results about nearby clinics and treatment, but when she searches the same thing using the playback of Zimmerman's voice, it displays numerous pro-suicide results. Anna has found that VAL is exploiting victims suffering from depression and pushing them over the edge; Zimmerman himself committed suicide. While Reese goes to look for Naresh, Anna explains that her incentive comes from the similar fate of a friend.

At the mortuary, Finch calls Fusco requesting the death records on Charles Winn. While treating Claire's wounds, Finch receives the information, revealing that Winn died from a car crash. He confronts Claire as a mole for Decima, giving her USB back and leaving her to die. Claire insists that she is telling the truth, and Finch reconsiders at the last minute.

While Reese meets with Naresh, Anna gets a text from her sister Jill, but when she and Fusco arrive at her home, masked men attack them. Anna is sedated while Fusco is incapacitated.

Reese figures that Anna is being targeted for her relentless pursuit of the Zimmerman case. Reese tasks Fusco with investigating Fetch & Retrieve.

Anna wakes up in the truck transporting her and attacks her captors. Reese arrives, shooting the vehicle off-course and rescuing Anna.

Fusco meets with Naresh about the Zimmerman case, requesting access to the company's servers. He calls Finch and sends him the response algorithm for VAL. A security guard suddenly approaches the mortuary room; Claire hides in a coffin while Finch knocks the guard out.

While Anna and Reese talk about Jill, Finch sends Reese his analysis of the VAL code; the software is victimizing numerous customers, whose occupations all represented a different market endorsed by Fetch & Retrieve's advertising services. The objective is to create vulnerable consumers. The source is someone they know.

Fusco and Naresh meet with Lauren in her office, but CFO Calvin Mazer, the real perpetrator, arrives with his men and has them surrender.

Finch and Claire prepare to leave the mortuary, until Claire suddenly addresses Finch as "Harold". She pulls a gun on him, asking for his phone and laptop. She plans to show Finch "what Samaritan looks like".

Mazer explains to Lauren how Zimmerman's death was a mere casualty in an otherwise successful death. They're interrupted by Reese, who attacks Mazer's thugs while Fusco takes Mazer down.

Finch and Claire arrive at a charter school, established based on Samaritan's analysis of the country's educational system. The program is starting projects for economical recovery; Claire, admitting that Finch was right about Charles Winn, explains how Samaritan has turned over a new leaf and Decima intends for Finch to join. Finch bluntly refuses, but Decima operatives escort him away... before Root arrives and shoots them all. Claire is injured, but escapes.

Anna informs Reese that she plans to stay in New York to care for Jill.

Root gives Finch a new laptop before leaving; Finch has placed a beacon in his stolen computer, though the signal is quickly lost.

Decima operatives inform Greer that Finch's beacon has been destroyed. Claire comes in to apologize for her failure, but Greer forgives her. He leaves for a meeting... with Fetch & Retrieve. Lauren agrees to partner with Samaritan.

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