Moments pages are Spoilers Off. All spoilers are unmarked.
- In the Progressive ending animation, we scroll across a long shot of the original FLCL cast with the new cast from Progressive and Alternative. We haven't forgotten about you, and welcome to the family, everyone.
- Also in the ending animation, after Haruko steals Atomsk's power, two familiar characters look up at the sky: an older Naota and Mamimi.
- Only two episodes in and compared to the manipulative and abusive relationship between Naota and Haruko, Jinyu is actually trying to watch out for Hidomi in spite of attempting to kill her previously. Best shown at the end of the episode in that rather than trying to harm her or thinking she's some sort of abomination for her transformation, Jinyu just opts to grab an exhausted and injured Hidomi and gently set her up for a medbay without a second though, compared to Ide's being tossed in.
- Hidomi smiling and laughing with Ide at the end of Episode 2.
- After Naota getting jerked around by a Manipulative Bitch and a Cloudcuckoolander using him as a surrogate for his older brother (both of whom were also way too old for him), Ide and Hidomi have the healthiest relationship seen yet in FLCL, with Ide being a genuinely Nice Guy willing to risk his life for Hidomi (even if he's largely ineffectual) and Hidomi's stoic nature faltering whenever she's around him.
- The fact that Julia Jinyu, who genuinely cares for the safety and well-being of others, is actually part of Haruko that split off after they absorbed Atomsk, proves that despite her manipulative tendencies Haruko really did care about Naota in the end and realize that trying to gain Atomsk's power by destroying the world was wrong. Unfortunately, it only takes a brief conversation with Jinyu before Haruko gets pissed off and unceremoniously eats her just to stop listening to the moralizing.
- Although Iide couldn't do very much, he makes a valiant effort to fight against Haruko in episode 5 now that Jinyu isn't there to protect either himself or Hidomi.
- There a lot of these in episode 6:
- The reveal that Aiko is an Artificial Human created from Canti's parts comes along with her "father" explaining that he couldn't bring himself to use her as a weapon. For however long she was with him, he had become fond of her. The last thing he does before mochi-fying, is pass her a piggybank and saying she is free to do whatever she wants.
- Hidomi and her mom reconcile and decide to run the cafe together, not because it is where her father is (not) coming back to, but because it is their home. They hug each other through Aiko/Canti.
- Atomsk embraces an angry, frustrated, and heartbroken Haruko. Then, he leaves again, but not before leaving Jinyu with Haruko.
- After Aiko's Fetal Position Rebirth from the giant pumpkin, Mori catches her as she falls. He then loans her his oversized shirt to cover herself with.
- Hidomi and Ide Holding Hands in the final scene. It is Sealed with a Kiss.
- Episode 1
- The four friends hanging at school, laying on each other while talking.
- Building the rocket together; it's picturesque childhood bonding.
- Episode 3
- Even though she had Secretly Selfish motivation, Kana jumping to help Mossan is a great example of friendship. Covering a work shift wouldn't be fun, after all, and she's not getting paid for it either.
- At the contest itself, Haruko engages in her usual outrageous hijinks, but it doesn't have anything to do with Atomsk or even manipulating a robot or guitar out of someone. It's to promote Mossan's dress design, which she models herself. It's basically a Cool Big Sis stunt.
- Episode 4
- Episode 5
- The only personal effect in Pet's room is a photo of her and Kanon when they were younger.
- Episode 6