Why did Stan let the Jennings go?
For six seasons, we've awaited the confrontation between FBI counterintelligence agent Stan Beeman (Noah Emmerich) and his across-the-street neighbors and best friends, the Jennings. Poor Stan, oblivious to the goings on in front of his nose; unaware that the family he came to love, the people he respected most of all, were his secret enemies. But as was inevitable, Stan starting catching on. When Philip and Elizabeth left town on Thanksgiving, blaming the failings of their travel agency, he found the excuse suspicious. Who leaves their family behind on such an important American holiday? And after a botched KGB mission in Chicago, Stan's spidey sense went into overdrive.
There were many ways this confrontation might have played out. Stan, occasionally prone to outbursts, might have killed them. Elizabeth, with all of her fire and drive, might have killed him. Or Philip, in an attempt to save his wife or friend, could have turned on either. But what actually happened was totally unpredictable and completely perfect: Stan let them go, and they went.
The scene takes place in a parking garage near Paige's school. Philip and Elizabeth, aware that their time is up, collect their daughter and try to make a run for it. But Stan tracks them and approaches them in the concrete fortress, clutching his gun and demanding answers. After a brief moment of keeping up a lie -- that they were bringing a sick Paige back home -- Philip relaxed his shoulders and finally confessed: "We had a job to do."
After a back-and-forth, a gobsmacked and broken-hearted Stan stands frozen as his best friend, Philip, tells him everything, and admits they're leaving behind their son, Henry (Keidrich Sellati), and needs Stan to protect him. Philip's tearful confession, straight from the gut, is the reason why Stan does nothing. He watches as the Jennings flee in their car and he just stands there, out of things to say, lost in thought. These were his friends, practically his family, and even though he caught them, he can't break them apart. Not after all that they've given to each other as human beings -- outside of their jobs, beyond their service to their respective countries. Stan is probably thinking of Henry, the boy he's come to love like he was his own, and how his role in the Jennings' incarceration would destroy that foundation.
In the end, he makes the choice never to speak of the encounter, at least not to his employers at the FBI or to his partner, Dennis Aderholt (Brandon J. Dirden). When Aderholt reveals that Stan was right, that it was the Jennings all along, Stan says nothing of the pivotal confrontation, and acts like it never happened. "I'm gonna kill him," he says, knowing full well that he didn't, and that his heart won out instead.