'''Season 2, Episode 1''':
!The Contingency

->''I just wanna find my friend. See, I don't have many friends. [[OnlyFriend Just the one, in fact]].''

Following the previous season's cliffhanger, Reese picks up the phone and receives a message from the Machine: a seemingly-random string of words and letters. At the library, he manages to crack the cypher--it corresponds to the labels on the spines of the library books, using their Dewey Decimal System classifications to form the person's Social Security number--and gets the number of a down-on-his-luck accountant who [[PayEvilUntoEvil embezzled money from neo-Nazi drug dealers.]] Reese initially thinks the accountant will provide him a lead to finding Finch, but it turns out he's just another person who needs help: Finch's [[TitleDrop contingency]] is that Reese take over their mission and help the helpless alone. In the course of protecting the accountant, Reese decides he's had enough and tells the Machine he'll quit unless it bends its programming and figures out a way to help him find Finch. The Machine complies, giving Reese a new number, and he goes on to take out the neo-Nazis. Afterwards, Reese tracks the new number to a fourteen-year-old girl who disappeared many years ago from Corpus Christi, Texas; he suspects this girl is Root.

Meanwhile, Carter takes over the investigation into Alicia Corwin's murder, but she's not the only one taking an interest. Denton Weeks of the NSA is summoned to Washington by his superior "Pennsylvania Two" (previously seen directing the assassins in "No Good Deed") and told that in response to the death of one of their own, someone else will be taking over the Machine's oversight. One of the superior's goons infiltrates the NYPD and steals or corrupts the investigation files, giving Carter no other leads. At the episode's end, Reese visits her with the Corpus Christi lead and informs her they're both going to Texas.

Root and Finch are traveling south, with the former threatening to hurt innocent people unless things go smoothly. She commits a number of seemingly-random crimes, first robbing a pharmacy for particular medications and later using them to poison a woman in a restaurant in order to steal her phone and send her lover a message. Along the way, Root explains that after growing up in complete bewilderment of human behavior, she realized that people are a cosmic accident -- but the Machine is different. It was designed, and to be able to predict human behavior, it must be a little bit human itself. Root is enamored with the Machine and wants to "set it free". In the final stage of her strange crime spree, she and Finch break into the woman's house and wait for her lover to come home. When he does, he turns out to be Denton Weeks, summoned by the message Root sent, and Root knocks him out with a hypodermic needle.

In flashback, Finch starts testing the Machine's programming, running some "hide and seek" tests in the streets of New York and later taking his phone into a casino so the Machine can predict the best course of action. Afterwards, as Finch leaves the casino, the Machine sends him a "stay" message via mobile phone and it saves him from being hit by a drunk driver. Finch takes the Machine to task, and programs it to put the safety of others above Finch.

!!Tropes in this episode:

* AccidentalTruth:
--> '''Old man''': Somebody out there must like you, my friend.
* AIIsACrapshoot: Root actually wants to invoke this. "Humanity has gone as far is it's going to go. I want to see what happens next."
* AndYourLittleDogToo: Root makes it clear that if Finch calls for help, she'll kill not him but an innocent third party.
* AIIsACrapshoot: Root wants to set the Machine free of its constraints.
* AngryGuardDog: Reese gets the neo-Nazis' dog to [[HeelFaceTurn come over to his side]] because it's a military-trained dog, and Reese knows the proper commands.
* BattleDiscretionShot / DestinationDefenestration: Reese taking down the Aryan Brotherhood gang.
* BookEnds: Reese TrespassingToTalk to Carter.
* BoundAndGagged: With bondage gag balls too.
* CallBack: Several to the Pilot episode, notably [[MeaningfulEcho Reese quoting Finch]] to himself while working in the Library.
-->''I gave you a job, Mr. Reese. I never said it would be easy.''
* CardSharp: Finch briefly becomes one thanks to the Machine's card-counting skills. Of course, at the end of the evening he deliberately loses all the money he won so that nobody realizes that he was cheating.
* ContinuityNod: Carter returns the bag of weapons Reese gave her in "Flesh and Blood".
* ConvenientlyTimedAttackFromBehind: Carter coming to Reese's rescue at the end.
* DrunkDriver: Nearly runs down Finch at the casino in one of the flashback scenes.
* FirstNameBasis: Fusco notes that Carter has started calling Reese by his first name.
* FriendshipMoment: Lots of them from Reese, to the point of blackmailing a sentient supercomputer in order to save his OnlyFriend.
* FreudianThreat: With a dog and a pair of hedge clippers.
* GameOfChicken: Reese is about to be assaulted by armed neo-Nazis and he will only run out of danger if the Machine helps him find Finch.
* GiantMook: Titus was HUGE, okay?
-->'''Reese:''' Pick on someone your own size...well someone a little...closer to it.
* [[HesDeadJim He's Dead, Leon]]: Reese points this out.
* ImprovisedWeapon: Reese knocks a BadassBiker off his motorbike with a fire extinguisher.
* ImpliedDeathThreat
-->"I might be hard to reach for a few days."
-->"Denton, we can ''always'' reach you."
* InflationaryDialogue: Leon, when Reese asks him if he's sure he lost all the money.
-->'''Leon''': No, I'm... I'm pretty certain. ''[Reese squints at him]'' Like, 80% certain. ''[another look from Reese]'' Maybe 75% certain...
* JerkassBall: Reese never was particularly nice to Fusco but he takes it UpToEleven in this episode as he races to find Finch.
-->'''Fusco''': "John"? We're on a FirstNameBasis?
-->'''Carter''': What do you call him?
-->'''Fusco''': Bane of my existence.
* MachineWorship: Root's description of the Machine is somewhat... ''loving''.
* MoralityChain: Fusco says he doesn't want to see what Reese will become without Finch holding him back.
* MrExposition: Reese starts talking to himself as he tries to figure out what is going on and what the Machine wants him to do. It is a sign of how much he has grown to depend on Finch as his MissionControl. This really freaks out the [=POI=] as well as the bad guys.
* MyFriendsAndZoidberg: Reese reluctantly adds Fusco to his list of friends when he makes an annoyed grunt (due to his gag).
* NotSoDifferent: Root spends most of the episode making this comment to Finch. Eventually, he concedes that she's right -- which is why he knows it's important to keep the Machine out of her hands.
* ObligatoryJoke: Reese's "gag order" gag re the gag in Fusco's mouth.
* OnceForYesTwiceForNo / HowManyFingers: Finch communicating with the Machine.
* PayEvilUntoEvil: What Leon is doing to the neo-Nazis.
* PreviouslyOn: From The Machine's perspective, replacing the usual OpeningNarration.
** FridgeBrilliance: There's no OpeningNarration by Finch in this episode (and "Bad Code") because Finch is absent from his usual place at the start of the episode.
* PunchPunchPunchUhOh: Reese runs across this for the first time when fighting a seven-foot-tall neo-Nazi bruiser.
* ReedRichardsIsUseless[=/=]MisappliedPhlebotinum: Lampshaded by Root; the true implication of the Machine is not its potential misuse as a tool of Big Brother, but that to successfully predict human actions, Finch had to have created ''artificial intelligence''. Root can't believe that Finch's response to doing this was to BlackBox the system and hand it over to a corrupt and power-hungry US government, and is determined to set the Machine free.
* RoaringRampageOfRescue: Try and stop Reese from finding Finch. I dare you.
* SlippingAMickey: Root grinds up a drug she's stolen from a chemist and slips it into a woman's drink (she's addicted to painkillers, so it's probably meant to look like an overdose). When the woman collapses, Root uses the distraction to steal her mobile phone as she's TheMistress of her target, to whom she sends a text to [[ComeAlone lure him into a trap]].
-->'''Root:''' She'll be OK. [[BaitAndSwitchComment In a few months.]]
* StaringDownCthulhu: It takes a certain kind of defiant badassery to stare down an omniscient sentient supercomputer until it does what you want.
* TattooedCrook
* TrojanPrisoner: Reese allows himself to be taken prisoner knowing they'll take him to the men who are holding Fusco and Leon.
* {{Ubermensch}}: Root all but uses the word when describing herself to Finch.
* WalkInChimeIn: The Aryan Brotherhood does this a lot.
* WeNeedADistraction: Root [[PalmBloodletting slices open Finch's hand]] to distract a chemist so she can steal medical supplies.
* WhamLine: Although implied in the previous season, Root confirms that the Machine is a fully-fledged Artificial Intelligence.
--> '''Root''': I don't want to control your machine... I just want to set it free.