In vs. Youtube, while the Youtube face is gloating after undoing the Second Coming's near victory with a refresh, the Second Coming is huddled on the ground holding his face in his hands, clearly at a loss.
Everyone mourning Green's (apparent) death in PvP, especially Orange. When Green respawns from the original "Stick Figures Fight" window, he finds everyone building a memorial shrine for him and laying down flowers.
At the climax of The Virus, the titular ViraBot eats the Animator's mouse cursor. He tries to retrieve a new one like he did in 4, only for ViraBot to destroy the start menu. He's already seen that ViraBot can dissolve anything with a single bite. At that point he's completely powerless to protect his friends against this monstrosity, and it certainly looked like ViraBot was about to kill The Second Coming before The Chosen One entered the scene.
In "The End", when faced with a Friend or Idol Decision, Purple chooses to go for the Dragon Egg rather than save Blue and Green about to fall into the void. As they watch the "Levitation" effect timer tick down, the two of them toss their crowns into the void and embrace in one last hug.
At the end of The Chosen One's Return, the Chosen One succeeds in defeating the Virus, but he opens up a portal to leave, either because he has to return to wherever he had been roaming before his return, or he still cannot help but feel as if staying in the Animator's computer takes away his freedom due to past events. Also, the state of the computer is devastatingly ruined.
Similar to the vs. Youtube moment, near the end of vs. League of Legends, Purple's worm-creature is destroying everyone else's main crystal while everyone sans Second Coming is lying nearby in defeat. Green struggles to stand at one point but fails, and when Red tries to continue to fight back, Green stops him; subtitles or no, it's clear they all think it's a lost battle.
In SkyBlock, The Second Coming begins to miss the others after he opts out of their decision to go through one of the portals shown at the end of The End. Made worse when he tries to go help them and is cut off by a Ghast deactivating the portal with a fireball, forcing the Second Coming to jump into a different portal to save himself on top of trapping the other stick figures in the SkyBlock universe, separating them indefinitely.
Prior to that, the scene with everyone huddled cold and starving around a campfire is just heartwrenching.
In TNT Land, Red is pushed of the ledge and falls into the void. His friends are understandably distraught, until it's revealed that he survived, thanks to an ocean underneath.
In The Dolphin Kingdom, after barely surviving a Drowned attack, Green actually breaks down crying, thinking that they will never find the Second Coming again. Again, it's mitigated, since it's revealed that the Second Coming is literally only a few blocks away from them. In addition, Alan decided to be a Trolling Creator and make it look like the scene was gonna end with them still separated like that. (Fortunately, it continues long enough for them to reunite.
Even worse when you remember that Green was the one that disagreed with the Second Coming about whether or not to go through the portals at the beginning of "SkyBlock". While that last meeting was amicable enough that we can likely assume there was no Parting Words Regret, it's easy to imagine that Green is really regretting not listening to the Second Coming and backing out of the adventure.
Similarly, the prior scene with the Second Coming has him pull out his picture of his friends and forlornly hug it, after he was forced into yet another different portal by Nether mobs.