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The CSI Effect: Winked at in S01E14, "Wolf and Cub", when Carter tells a perp they have DNA back over the course of a few days. He, being a Genre Savvy repeat offender, coolly retorts that those take three months to come back.
Foe Yay: In the opening of "Legacy", Carter waiting for Reese looks a lot like someone waiting for their date.
Fridge Brilliance: How does Finch know who he can safely call for backup when Elias is breaking into the safehouse? Thanks to his work as Reese's inside man in HR, he knows just about everyone who isn't an honest cop in New York, and called somebody who wasn't on that list.
Ho Yay: Reese wakes up to his second meeting with Finch handcuffed to the bed in flexcuffs.
Moral Event Horizon: Elias locking a baby in a freezer car to get Reese to reveal the location of a man Elias wants dead. This is actually a double MEH - not only is Elias threatening to kill a baby, he had agreed to help Reese save the baby from some kidnappers as a return favor for Reese saving his life in an earlier episode, which shows how Elias honors his debts.