A little bit of angst, a whole lot of crack, and Animated!Galvatron...
1. Any continuity, but G1 or Movie probably work best. The local wildlife around Autobot HQ starts to die off. Mammals, birds, reptiles, and insects--everything is dying. Worse, tests indicate that the humans who spend the most time around the Autobots have all developed cancer. Everyone suspects that the alien robots are producing some unknown kind of radiation that is killing the local wildlife. In an effort to protect Earth's indigenous lifeforms, the Autobots leave the planet. And that's exactly what the Decepticons had planned all along. Whether the humans catch on in time and/or have real cancer or fake cancer is up to the writer.
(Inspired by the way Ozymandias manipulates Dr. Manhattan into leaving Earth in the Watchmen comics. I haven't seen the movie, so I don't know if it's different there.)
2. Animated. I do believe that Isaac Sumdac loved Sari, but he's a scientist and I can't believe that he didn't at least run a few tests on her to figure out what she was and if she could be duplicated. One such experiment has a few of Megatron's more violent tendencies and the ability to transform at least one arm into a BFG. Said experiment is mostly human in appearance, but is clearly a technorganic "heir" to Megatron. It escapes and leaves Earth. The Decepticons who are still at large are a little unsure, but mostly willing to listen. Hey, it's better than taking orders from Starscream's ghost, right?
FYI, in my mind, the Animated Galvatron is female and resembles a more Sari-ish "Gal" Gardner, a picture of whom can be seen
here. Gal is the result of Green Lantern Guy Gardner being turned into a woman, just in case you're wondering. The guns are very Decepticon-y, y/n? It was a discussion of the Guy/Gal thing that inspired this bunny in the first place. However, anyone who adopts the bunny is free to disregard this, of course.
3. Any continuity. Let us pause for a moment and consider all of the cracked-out shenanigans that go on among fans. Not cosplay or role-play, those hobbies are relatively tame. But otherkin ("I'm not human, I'm a dragon/elf/vampire/alien trapped in a human body."), soul-bonders ("I am the reincarnation of [insert fictional character here]."), the other type of soul-bonders ("I married [insert fictional character] on the astral plane and/or my soul is magically connected to [insert fictional character]'s soul."), and the third type of soul-bonders ("I am actually the bastard love-child of Sailor Moon and Dracula.") are often considered odd, even by the most open-minded fans.
What happens when in-universe humans start doing this stuff? And you know they will. This planet really is that crazy. So what happens when people show up who claim to be Cybertronians trapped in human bodies or the reincarnation/astral-wife/bastard offspring of a Transformer? How do the humans explain this madness to the Autobots?
4. G1/Shattered Glass crossover. This one's for the Perceptor fans. There was a Perceptor in the Shattered Glass comics, but he was killed (according to the wiki). This seems like an excellent time to introduce Shattered Glass Magnificus. Remember
Magnificus? He's the black repaint Decepticon counterpart of G1 Perceptor who comes with
Ga'mede, his alien bishounen boy-toy. In the Shattered Glass continuity, they would be good guys. So it would be especially interesting if Shattered Glass Magnificus and Ga'mede were introduced to the G1 characters.