- Alternative Character Interpretation: Are the humans who go nuts at the end being driven mad by Gaia, or did they just go stir crazy because Seno Miyagi declared that they would never return to Earth? Given the mystifying nature of the last episode, it's kind of hard to tell.
- Common Knowledge: It used to be very common for fans to assume that the English ending theme was sung by Laura Bailey, the voice of Marlene. It was later revealed to actually be Daphne Gere, who also sang the English Dragon Ball ending.
- Designated Hero: Gaia is supposed to be the Big Good who wants to protect the planet from the destruction that humans have brought... except Gaia decides to do this by creating a race of Big Creepy-Crawlies to destroy modern civilization and kill scores of people, out of the belief that technology and overpopulation are what is ruining the environment. The humans are basically supposed to be seen as the villains for defending themselves. Not only that, but when humans actually try to make things better by building a Space Station to ease the strain on the planet, Gaia responds by corrupting two of their best soldiers and having them massacre nearly everyone inside, then afterwards drives the rest of them insane and blows up the colony.
- Designated Villain: Humanity itself is eventually portrayed this way, where the Earth itself is spawning the Blue, horrific monsters, for the sole purpose of killing all humanity for daring to develop technology that elevated humans above the natural order (and also overpopulating). In particular, the leaders of the space colonies, Chairman Victor and the High Council, are demonized and portrayed as the Big Bad for the grave crime of wanting to leave the bug-infested Earth (which had apparently decided to kill them all itself) behind for good and wanting to keep technology around, while Seno Miyagi and his group of humans who try and flee Earth to settle on more hospitable planets elsewhere in the galaxy are portrayed as the worst of the worst, and all of them wind up going insane and “karmically” dying.
- Esoteric Happy Ending The ending could only be considered happy if you're a severe technophobe. A few humans have survived Gaia's Vengeance, and they can all live in harmony with mother nature, free at last of technology! Then the Fridge Logic sets in - the only survivors will be physically strong people. If you're a person who is crippled, blind, deaf, has a curable terminal disease, etc. then you're hosed. Mother Nature hates you and you have no right to live. And those well-meaning humans, who were trying to save the planet by living in a space station (to ease the strain placed on Earth) and eliminating the hostile creatures that had infested Earth? Screw them.
- Growing the Beard: For quite a few fans, the series improved sharply around episodes 10 and 11, when Yuji and Marlene escaped to space.
- Inferred Holocaust: So humanity has had all of its technology taken away. We're supposed to see this as a good thing-except that without things like science and medicine, humanity is at best destined to be stuck in an eternal dark age, and at worst doomed to go extinct.
- Memetic Mutation:
- The Blues looking like an "Angry Woman's Crotch." An [adult swim] card referenced this during the first airing of the series, and while people had brought up allusions to Vagina Dentata with the Blue previously, this really exploded.
- The reason why they should have aired this on Toonami, not Adult Swim: STRANGE AND TERMINAL ILLNESS. Doesn't that sound like TOM?
- Moe: Alicia.
- Strawman Has a Point: Man is ruining the planet due to technological excess and overpopulation, and so nature sends the Blue to forcibly knock humanity back to the Stone/Bronze Age. Many of the humans in Second Earth are supposed to be seen as cold and heartless, and Chairman Victor of the High Council in particular is supposed to be the Big Bad, for fighting against Gaia and the Blue instead of learning to live In Harmony with Nature. The problem is that at the time of the show's events, humanity knows it's ruining the planet and is trying to fix things... an effort the supposed Big Good Gaia is actively sabotaging with the Blue. At the end of the series, Seno Miyagi decides he and the rest of the humans should remain on the colony and seek out other planets to live on, which is a perfectly reasonable argument at this point and would leave the planet alone, sparing it from further harm. Instead, Gaia drove the humans insane, Seno is shot dead, and Second Earth (which was built to ease the overpopulation) is destroyed, with the Green Aesop being that humans can live in harmony with nature, as long as they're not abusing tech. Sadly, "tech" here is defined as anything more advanced than the wheel.
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