- Hex's Heroic Sacrifice in Season 4.
- "Bob, I have always loved you. Dot, take care of him, and be happy..." *sniffle*
- The ending of "Web World Wars": Bob is shot into the web as Dot stares without being able to do anything other than scream Bob's name, then proceeds to close the portal. Heartbroken, Dot looks down, notices Bob's keytool that had Megabyte had just crushed and tossed aside on the floor, picks it up and painfully looks at it. Later, when queried about what happened to Bob, Dot simply says "I'm sorry" and places the broken Glitch on Enzo's hand, prompting the young sprite to scream a Big "NO!" before breaking into tears.
- Two moments from "Game Over":
- Megabyte orders his fleet to attack the principal office. The fleet is cut off and destroyed, yet the viral binomes go down fighting, the commander shouting his loyalty to Megabyte. Megabyte, huge Jerkass that he is, is unaffected, but Dot weeps over the slaughter.
- The ending. Made even worse by everybody's shocked silence (19 seconds, of everyone in the War Room just shocked and staring at Dot in disbelief and even mild incomprehension) after they hear the words "GAME OVER. USER WINS.", only to have it broken by Dot's grief-stricken scream.
- Surprisingly, Slash gets a minor moment when he laments the way things have been going in Mainframe lately."Bob always stopped us before we could do anything really bad. Now, nobody does."
- "Megaframe." The moment where Enzo, now Matrix, is reunited with Dot, usually starts the waterworks up pretty quick.Dot: [Stunned Silence]Matrix: Uh, hi..... sis.Dot: ...Enzo? [bursts into tears] ...Enzo! Oh, Enzo!!! [hugs him] I thought you were nullified! I thought I'd lost everything!
- One thing about Matrix and Dot's reunion that always seems saddening is the short look of confusion on Dot's face. Either she doesn't recognize her brother at first, or she's in denial that it's really him and it HURTS to see. Even worse, Matrix grew up at an accelerated speed so he's not supposed to be anywhere near as old - something that almost certainly hit Dot.
- The tracking shot of Mainframe in ruins, with Matrix, AndrAIa, Bob, Captain Capacitor, and Frisket just staring in horror. Worse when watching immediately after the preceding episode's triumphant ending of our heroes finally managing to make it home.
- Hex curled up in the Fetal position and shrinking away from Scuzzy at the end of "Painted Windows".
- Hex's reaction to her masks being fused together, effectively bringing her full sanity for the first time in her life.Bob: How do you feel?Hex: For the first time... WHOLE.
- Though it leads to a Happy Ending, in End Prog the forced system crash Bob implements by allowing the User to win a Game by keeping everyone out of it. The reactions from the Sprites and Biomes as their world is ending all around is devastating, especially an image of a Little Girl Biome, all alone without her parents or anyone, cradling her doll as the System Crash is announced.
- At the end of End Prog there's an musical preformed by binomes recapping the events of season 3. During the part where Enzo loses the game and is forced to start game hoping growing into a 'grim aggressor man' there's a cut to Matrix in the audience looking regretful and sad. One can tell that Matrix isn't happy with the person that he became.
- When Bob first arrives in Mainframe, its Twin City was just destroyed. There's nothing he can do to repair that sort of damage, save preventing things from getting any worse. Dot mistakes his condolences as blame for the accident, and brakes down in tears on him, all while Bob is pleading just to try and help her.
- While Enzo and AndrAIa are together at the end of her debut episode, that AndrAIa is a copy. The original AndrAIa left forever with the game cube and is all alone.AndrAIa: Goodbye, my friend.
- Frisket drained of energy by Gigabyte. Sure, Bob immediately reassures Enzo and AndrAIa that he'll be fine, but it doesn't make the horror of seeing their faithful companion downed in an effort to protect them.
- Enzo looking around for AndrAIa in "Between A Raccoon And A Hard Place", after it looked like the game had taken her with it. It's a brief moment, but the look of despair on his face and the tone of his voice as he calls "AndrAIa!" really help convey the desperation the young sprite was feeling.
- To save Mainframe, save the Net, from Daemon's infection Enzo has to shatter Matrix's first time feeling whole and content. Needs of the many and all, but considering the self-loathing that Matrix carries with him (as we saw in season three's "Number 7")... The fact that it takes Matrix going to the dark place that has defined his life to save the day...
Tear Jerker / ReBoot