This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / TRON: Uprising
Clu's attack on Flynn and Tron, with "Adagio for Tron" playing as Tron fights, is just as depressing as it was in TRON: Legacy. Doubly so because of Dyson's role in the fight.
The revelation that Cyrus, the kind and idealistic young guard who saved Tron's life and began the uprising eventually fell to corruption and had to be locked away. In the present day, he's deranged and insane, possibly from the solitude.
The ending to Welcome Home Dr. Keller was introduced in the previous episode, and much of this episode was of her desperate attempts to flee from the occupation, while Beck and Paige try and recruit her. In the end, she goes back with Paige to the Occupation, and is re-accepted, up until Tessler kills her.
"Rendezvous". After building up a legitimate connection between one another (including what may have been an Almost Kiss if Pavel hadn't interrupted them), Beck, unbeknownst to her, ends up getting rejected by Paige twice. After saving her as the Renegade, he tries to convince her to join him and switch sides, saying that he's fighting not only for the citizens of Argon, but her as well (And this happens, of all places, on the bridge she took him to on their first date.). She tells him he's already lost that battle and leaves. Then when she meets him as Beck, for a date he wasn't sure she would show up for, she stops him from coming any closer to her than half a pool table away, and tells him she can't be with him because her time with him made her grow soft and unfocused, and she leaves him alone again. Beck's appearance after she's done so the second time... rarely has he ever looked so utterly defeated.
"No Bounds", sooo much. In the course of one episode, Cyrus manages to utterly ruin Beck's reputation as the Renegade, turning his friends against him in the process, and kills Able by proxy (the final nail in the coffin for Mara). Now the garage is closed and Beck has basically nothing to go back to, only his rebellion which is that much more difficult.
"Terminal" contains a couple of doozies.
Cutler, resistance member and Beck's comrade-in-arms from "The Renegade" parts I and II, is revealed to have been caught by Clu's forces and Rectified. He manages to break his reprogramming all too briefly when Beck reveals himself as the Renegade...but the repurposing quickly takes control again, and Beck is forced to obey Tron's advice and let Cutler fall to his death. The look on Beck's face when he realizes that Tron is right and that his friend is gone for good is painful to behold.
Pavel's casual murder of Able's Bit. What a bastard.