While it's among the lighter series in the Gundam series, it's not without some darker moments.
- The initial invasion of Earth by the Moonrace's Dianna Counter forces counts as this. Which wouldn't be unusual for a Gundam show...except that Earth people are no more advanced than in World War I. From the perspective of someone on Earth, the realization that all your guns and biplanes do close to nothing against an entire army of mobile suits even after the titular Turn-A shows up and they find their own caches of Lost Technology weapons is downright terrifying.
- Corin Nander levels an entire city, killing hundreds and instantly turning thousands more into refugees, just because he thinks it'll get the Gundam's attention. Not just any city, either, but Nocis. It's chilling to watch the destruction of Bostonia Castle, which had been one of the series' central locations.
- Given his violent tendencies before, seeing Dianna traveling with Corin Nander as an escort, and then watching him interact with a bunch of children at a harvest festival, can put viewers on-edge. (Though, ultimately, his malevolence is directed only towards the White Doll.)
- When he sees the Turn X activate its Moonlight Butterfly, he has another Freak Out that is fully Played for Drama, and retroactively applies to all his previous nuttiness towards the White Doll, because this time, we see why: he's having a constant case of My Life Flashed Before My Eyes, and he always sees a specific figure that the White Doll reminds him of. It's the Wing Gundam Zero, all but outright confirming Corin is specifically a survivor of any of Wing Zero's battles, most likely Quatre's Roaring Rampage of Revenge in its debut.
- The depiction of a nuclear detonation in "Midnight Sunrise." Gavane Gooney's blithe assumption that the warheads are just more bombs adds another layer to Zenoa's utter terror at the discovery. It's mirrored by the Rett Team, who are equally unwilling to listen, with each shot increasing the danger. When the warheads are flung around, they strike the ground with an ominously heavy clang. Once Loran and Zenoa finally convince or force all the combatants to flee the area, the soundtrack is not one of the usual battle themes but an eerie vocal piece that sounds like an ancient priestess lamenting the gods' wrath... and when the denotation occurs, the lighting is exactly like the second sunrise that a nuclear bomb really creates. It's seen even as far away as the Soleil. And it all happens with the knowledge that Gavane's Borjanon was buried in a gully right next to the explosion.
- The Turn-A and Turn-X themselves are essentially walking Nightmare Fuel, much like the Ideon. In addition to outclassing just about every mobile suit ever made in the Dark History (while using only a small fraction of their full power), there's also the "Moonlight Butterfly" a nanomachine system that can destroy any technology, which was also responsible for ending said Dark History by destroying civilization on Earth thousands of years before the series takes place. There's a good reason why they're so feared.
- There's also the fact that the nanomachines used are capable of regenerating the mobile suit's pilot indefinitely. Given that Gym Giningham is trapped in the cocoon generated by the Moonlight Butterfly after the last battle, this also means that he'll be kept alive and conscious for all time.
- The implications of the Dark History are this and a tearjerker. No matter what the protagonists achieved in the other Gundam shows, it ultimately leads to the Moonlight Butterfly.