Dark Matters
- Phoebe's character arc. Dark Matters breaks a perky young woman who's excited about her powers into a deadly Renautas weapon dubbed "The Shadow" in the series proper. It culminates in her death by her own brother as he sees that she's been so broken that she's no longer his beloved sister. The actress has stated that Phoebe is a tragic victim of the dehumanization of specials.
Brave New World
- Claire and Noah had been estranged ever since her reveal, and they never got to reconcile the day of the bombing. And now that she's dead, they may never reconcile.
Odessa
- Rene's death. Noah desperately tries to save him but fails. He steels himself up and attempts to move on.
Under The Mask
- Luke's flashbacks of his family. It's quite clear that he deeply loved his son as he's working through his grief.
The Needs of the Many
- Molly's suicide. Taylor quickly loses her composure.
- Joanne leaving Luke after he reveals his ability, and her aiming a gun at his head for it. The look on his face as he said he'd let her shoot him and the look on hers as she realizes what she is about to do just drives in how damaged their relationship is and how terrible Luke feels about his powers.
- Joanne kills an evo who appears to be harmless, and has a family. That's sad enough, but then while Joanne and Luke are hanging about in said evo's home, a dog appears. It doesn't bark or growl; it just silently passes the two, walks over to its dead master and lies down beside him. The look on Luke's face is what really sells the moment.
- They just leave the body by the door. Now imagine the reaction the man's wife and kids when they get home and find him lying dead in front of them...
The Lion's Den
- Luke drives up to his old family home. It's quite clear from the abandoned mail and the photos of the once-happy family that how much Dennis's death affected him and Joanne. He spends the episode going through the family mementos and even torches the entire house, alongside his wedding ring, leaving with just the boat he and Dennis built together.
Game Over
- Phoebe kills Quentin. His last words:Quentin: Did I do it? Did I save her?
Noah: You did good, buddy.- It's made even more saddening when later Noah refers to Quentin as his friend, regardless of how much he got on Noah's nerves.
June 13th, Part One
- The whole episode, really. Claire dies in childbirth and apparently never told her own father that she was pregnant. The fallout from the bombing, including Dennis Collins' death, Claire dying during the eclipse, Phoebe Frady tortured until she created the eclipse. Angela promised to raise her great-grandchildren, but somehow is separated from them and apparently dies, leaving them to be raised separately.
June 13th, Part Two
- Because of Noah's impulsive action, Nathan has to lose all his life's memories, turning him into the moody, troubled teenager we saw in the first several episodes, who isn't even conscious of the incredible control he developed over the power of space-time teleportation and who has no idea he was raised by a loving family and got to meet his grandfather, Noah, and his great-grandmother.
- It's even worse for Anne, who probably hasn't been able to mourn her husband properly for the last year because Nathan doesn't remember him.
- Molly telling Noah that she'd rather die than give up the twins' location to Erica. All he can do is hug her and kiss the top of her head, already knowing she'll do just that in a year's time.
- Mr. Otomo realizing Erica's true colors and then bringing Miko to the real world, he's only able to spend a short time with her but the last thing says to her is he loves her.
Sundae Bloody Sundae
- Caspar's death at Joanne's hand. He essentially sacrificed himself to save Emily and Tommy from her.
Company Woman
- Joanne's death. Yeah, she was a total psychopath, but she's so far gone off the deep end in her grief that you have to feel some kind of sadness that her own husband had to kill her.
Project Reborn
- Noah dies by sacrificing himself as a conduit to allow Nathan and Malina's powers to work at full power.
- Luke also sacrifices himself in order to stop the first flare. He may have started out as a villain, but in the end, he was a hero.
- Quentin is forced to kill his own sister to save Malina when he realizes that she's too far broken to be saved.
- Quentin's speech in the end of the episode about how evos are just normal everyday people trying to live their lives despite their special abilities and how they could just be anyone. All the more poignant since he was forced to kill his own sister and saw how horrible people treated evos the whole series.
