- The early episodes of the animated series that dealt with Elyon abandoning her friends, parents and whole world as a result of brainwashing, especially since it took most of one whole season to resolve, instead of just being a fluke. It's like all those scenes from An American Tail, where Fieval almost finds his parents, all over again. Worst of all are the moments that dealt with Cornelia's relation to Elyon; when they threw out a Rosebud to a character who had up to that point been portrayed as consistently superficial, rude, and obnoxious, and she actually showed deep concerns about wanting to help her friend out of trouble, her teammates rejected her pleas.
- "E is for Enemy". When Susan laments to Will about her having sleepover and not asking permission and not feeling sorry about it. The girls have better reasons for it. The viewers know the real reason. But Susan doesn't. She believes that what she is saying is the cold truth, but it isn't. Then, the expressions on the girls' faces when they see Will's expression. You can just tell they won't to say something to Will's mom. Just wanna hug Will and tell her it's going to be alright.
- "F is for Facade". When the girls fight Nerissa's lackeys to rescue the kidnapped warriors. The remaining warriors inform the Guardians that Caleb and his father had supposedly been killed off by Nerissa, much to Cornelia's grief. When everyone walks back to the kingdom with a feeling of defeat, Cornelia suddenly drops to her knees and cries in despair over Caleb's death. The other girls run back to try and console her.
- Just these words from Irma to Blunk in "G is for Garbage": "Garbage! Worthless garbage! Like you!" What makes it worse is that Irma only said it out of frustration and the look on her face is enough.
- "H is for Hunted". Will creates an Astral Drop of herself to do her laundry while she helps her friends prepare for a party. Astral Drops are normally unable to feel emotions, but when Nerissa changes Will's Astral Drop into an Altermere, it gains all of Will's emotions and memories, including her attachments to friends and loved ones. Excited about her new life, Altermere Will has fun at the laundromat before eating all the food in the Vandoms' fridge. Her new zest for life immediately extends to Will's mother, who the Altermere sees as her own mother. She happily hugs Ms. Vandom before inviting her to the party at the school. When Will realizes how much trouble the Altermere is causing, she and the other guardians, thinking it's still a normal Astral Drop, begin chasing it down in an attempt to absorb it back into the Heart of Kandrakar. The Altermere, who loves her new life as much as anyone would, reacts violently, and a vicious fight ensues between Will and her. After the Altermere desperately explains to Will that she has feelings and emotions, Will then breaks down in tears, embracing her tightly and promising never to absorb her. However, Nerissa uses the distraction of the emotional display to fire a burst of lightning at Will, and the Altermere sacrifices her life to save her creator. A tearful Will offers to absorb the Altermere into her being, which would allow its experiences and memories to remain intact. The Altermere accepts and fades into Will's body, becoming one with Will's consciousness.
- "L Is For Loser", Narissa torturing Kor (aka Mr. Huggles) when he refused to harm Matt.
Matt: Stop! Your hurting him!
- "M for Mercy", where Nerissa invokes the soul of the ex-leaderess of CHYKN, Cassidy the Guardian of Water, to try convince her come back to life through Nerissa's magic. Cassidy has even forgiven Nerissa's murder of her, so she's got no regrets and refuses Nerissa's multiple offers... until Nerissa visits Cassidy's still living mother, Emily. Cassidy going all "... Mom..." when she hears Emily say she still misses Cassidy, only to become Nerissa's brainwashed puppet as soon as she cries and wishes to come back and be with her mom.
- "O is for Obedience" for Caleb, When he learns that Nerissa is his mother the look on his face afterwards really says it all. The scene at the very end where he brushes off Cornelia's sympathetic hug and walks off into the distance is particularly heartbreaking.
- Hay Lin's Heroic B.S.O.D. in "T is for Trauma". Seeing her so depressed and not as happy and vibrant...excuse me.
- Will's segment in the "Heart of Kandrakar" special, where we find that Will's friends in Fadden Hills effectively dumped her because her parents were divorcing.
- The brief fight between Irma and her mother Anna from "Water Shadows" (#25) leads to a bit of an emotional Wham Line. They're yelling at one another, and Anna tells Irma "You don't talk to your mother like that!" Whereupon Irma snaps: "Right! My mother!" The utter look of devastation on Anna's face is heart-wrenching, as is Irma's immediate reaction of guilt and regret — especially since this is how the comic reveals that Anna, despite the resemblance, isn't Irma's biological mother. Thankfully it's followed up by a Crowning Moment of Heartwarming where they reconcile and Irma shows that she does consider Anna her mother.
- The death of Will's pet dormouse. Especially after all she went through with her Jerkass dad.
- Cedric's death in the fifth saga, just after he had become a sympathetic character and fallen in love with Orube.
- In issue #82: Energy, Will remembering all her friends. Especially Taranee, which shows a small bit of dialog from issue #1.