Moments pages are Spoilers Off. All spoilers are unmarked.
- The horrifyingly depressing imagery of the opening Dream Sequence of the season. The first we see of Hidomi, she is envisioning herself in the destroyed ruins of her city and claiming that the only way for the world to become beautiful is after it is destroyed. That is merely the tip of the iceberg. She starts to see herself rotting away and chunks of her flesh and blood begin sloughing off and tumbling to the ground in heaps, exposing the bones in her thighs, leaving her arms stumps, and her chest flaking away. Who would have imagined it would start off so dark? Thankfully, Hidomi's body regenerates from N.O. and transforms into a Medical Mechanica robot, and things take a turn for the badass, and again, this is All Just a Dream.
- Hidomi's mother, Hinae, mentions that Hidomi's father has been absent for a while and they miss him, but she also wonders if they should stop waiting for him.
- Canti stopped functioning at some point between the first and second seasons, and has been cannibalized for parts by Eyepatch and Marurao. The two of them abusing his body certainly doesn't help.
- Jinyu getting killed when Haruko eats her and reabsorbs her. Now no one is left to protect Hidomi, just like in the original FLCL.
- According to Genki Hidomi, while her father is missing and perhaps because her mother is emotionally distant in expectation of his return, she has no mother either.
- Haruko's Villainous Breakdown against Atomsk when he rejects her a second time. Even though she's far from a good person, seeing Haruko break down crying is surprisingly tragic.
- Hana's reaction to the girls' rocket being ruined. All that work for nothing...
- In the climax of episode five, Kana is trying to rescue Pets when suddenly Pets explodes in raw anger at her as Kana was trying to say that they're friends, thus she should open up to her. Pets is very quick to begin screaming out that Kana is a hypocrite with an absolutely brutal "Reason You Suck" Speech deconstructing Kana's friendship with her and the others as being rooted in inherently selfish desires. It's incredibly sudden and the fact that it hits the nail on the head so hard causes Kana to freak out at the realization. While she's still able to save Pets, she subsequently passes out and has a dream about Pets not having to go to Mars so they can remain friends. In reality, Pets is still so upset that she has spent the past few minutes just glaring at Kana laying on the ground. Haruko asks Pets if this is really what she wants, with Pets silently walking away in response.
- The worst part is that it happens for fairly realistic reasons. Yes, even with Haruko punching a giant robot in the background. Pets isn't a Jerkass for seemingly no reason, but rather because Kana choose an already high-stress moment where Pets' life was in danger to interrogate her life-long friend about why she didn't tell her that family was leaving for space. This was also the culmination of Poor Communication Kills, from Pets never admitting any of her true feelings to Kana and Kana never paying enough attention to her best friend's life. It was the type of falling out that could happen between friends on any bad day and could potentially be resolved with enough time after tensions cool. At least, in any other scenario. In this scenario, though? After the finale is said and done, there's no implication of whether the two of them will ever even see each other again, much less reconcile.
- By all appearances, Pets probably gets the worst ending out of any character in any FLCL series. Not only has she cut ties with her only friends, with her last conversation with her best friend being a rant about how much she regrets ever meeting her, but she's now stuck on a different planet with the same abusive family that forced her to leave these friends behind and are the cause of many of her issues in the first place.