When Marty first meets with "Citizen Brown Universe" Biff, you find out that Biff is forced to be a good guy and follow all the rules or else. At first, you don't seem sorry for him as now he's not the evil bastard he was like in the past movies and previous episodes, looking to be a changed person for good. But you can tell that he regrets dearly being a Citizen Plus by the way he talks, especially when he gets to the part about giving up his many dogs, you can't help but feel sorry for him.
A minor example comes in "Citizen Brown", with (as Marty looks on from below) the DeLorean falling out of the billboard and smashing into the ground. While not as bad as seeing it get crushed by the train in Part III, it's still a smack to the face to see the DeLorean get wrecked... again. Marty, already marooned without Doc in a less-then-ideal alternate timeline, can only yell in frustration and grief at the sight.
It's hard to watch Citizen Brown struggle with what he's done. The road to Hell is paved with good intentions, indeed. Thank God for Doc's notebook...
When you finally manage to get Citizen Brown to believe that you're from an alternate timeline, what is the very first thing he asks? "In this... other world, the one you say you come from... am I... am I... happy there?" And he has this desperate look on his face.
When Citizen Brown asks Marty to explain himself, one of the options the player can pick is "I'm not supposed to be in this timeline." By clicking that, Marty calls Citizen Brown his "best friend in the whole space-time continuum" which he immediately begins to doubt.
Episode 4: "Double Visions"
Citizen Brown aka Alternate Doc's Face–Heel Turn as he doesn't want Edna to become a Crazy Cat Lady is very sad for Marty, as well for the player. This can be a What the Hell, Player? as well, considering the shady lengths Marty goes to in order to break Edna and Young Emmett up.
After Marty breaks up Emmett and Edna, Emmett hides up on the clock tower ledge, and sings a couple lines from Trixie's "I Don't Care" to himself.
In addition to that, Marty is trying to cheer up Emmett about listing things Emmett cares about. Marty lists himself and slips up by calling Emmett the name Doc. Emmett responds by telling Marty that he loathes him for ruining his life. Marty feels guilty, and while Emmett doesn't know who Marty truly is yet, it is incredibly sad and jarring to hear those words spoken to Marty by any version of Doc Brown.
Episode 5: "OUTATIME"
When Marty eventually gets Judge Brown to come around to seeing Emmett's point of view, he reveals that he himself had a strained relationship with his own father who disapproved of him coming to America. He implies that he and his father never fully reconciled before his death and he clearly fears that the same will happen between him and Emmett. This gets even worse when you realize that in the original timeline without Marty present, Doc and his father likely never reconciled, as indicated by Doc's remorseful recounting, which adds a layer of sorrow to Doc's character.
Citizen Brown being erased from existence as Marty is kneeling next to him. Granted, this is bittersweet as it leads to the normal Doc Brown being restored, but it’s still very tragic.
Before dying, he had his intentions of having his younger self and Edna paired again for the sake of making her happy, but after Marty reveals Edna as the speakeasy arsonist, all bets are off and Citizen Brown regrets his decision.
Citizen Brown: I thought I could change her; things could be different.
Having to see the completely rusted and dead DeLorean in Alternate 1931. It's one thing to have to see the car, a staple, a character, an icon, of this franchise get trashed in Part III, but to see it rust off into a wreck, a hollow, decayed and empty shell of its former self, its parts stripped, to make a clunky and rudimentary alarm system, is a real punch in the guts. Imagine encountering the long decayed web-covered skeleton of Bugs Bunny, or Mickey Mouse. Even Marty says, half-choked, "I hate seeing it like this". If Doc's talked to while looking at it, he'll just quietly ask Marty to not speak as he stares at it in shock.
