Ambiguous Situation: In his desperation to keep Kaon running, Megatron throws Sunstorm, Ramjet, Shockwave, and Blitzwing into the reactor to power it, Lugnut jumping in of his own accord. It's unclear if doing this actually killed any of them though, as while Megatron previously used Starscream's head to power the Omega Sentinels and he survived, he has Resurrective Immortality thanks to the Allspark Fragment in his head. Further information about Season 4 suggests that at least Lugnut, Blitzwing, and Shockwave were meant to survive and this was setting set up an arc where they strike out against Megatron, ultimately allying with Slipstream and a once again revived Starscream.
The Cameo: Scrapper and the Dinobots are shown on Dinobot Island as Kaon goes to crash, the implication being he and Snarl were having another confrontation with Grimlock and Swoop.
Deal with the Devil: The armistice between the Autobots and the Decepticons. In exchange for going into exile, the latter would be absolved of any and all war crimes they committed during the Great War.
Felony Misdemeanor: By the end of the trial, the only crime that could stick to Megatron is attacking a spacebridge crew, which Sentinel bitterly notes is the equivalent of a parking violation.
Friend-or-Idol Decision: Bumblebee is ultimately forced to choose between his friends and his dream of joining the Elite Guard. He chooses the former.
I Choose to Stay: Bulkhead stays behind on Cybertron to help in the Energon farms.
Killed Off for Real: Ultra Magnus succumbs to his injuries dealt by Shockwave, and goes offline after having one final conversation with Optimus.
Loophole Abuse: Rattletrap is able to use this to deflect the worst of the charges against Megatron. When he asks Bumblebee to point out on a map the location of Earth (the planet where the majority of Megatron's crimes took place), 'Bee explains that Earth isn't in Autobot territory. As Rattletrap points out, since the crimes were committed outside of Autobot territory, then they're outside Autobot jurisdiction as well.
The Mole: Ironhide is assigned to Optimus's team by Sentinel so that he can keep watch over them, an assignment he's not too sure about after they end up back on Earth chasing down Megatron, and Optimus decides they should stay since Kaon is still sealed shut and they need to keep an eye on it.
Put on a Bus: Bulkhead and Arcee choose to remain on Cybertron once the team goes to chase after Megatron. In their place are Jazz, thoroughly fed up with Sentinel's actions and quitting the Elite Guard in protest, and Ironhide, having been tasked as Optimus' bodyguard and doubling as The Mole for Sentinel.
Retcon: In the original pitch for Season 4, Sari would have remained on Cybertron alongside Bulkhead and Arcee so as to continue her education under the latter and hopefully find more about her origins. Here, she joins Optimus and the team in chasing after Megatron and returning to Earth. TFWiki.net has it labeled as a continuity error for precisely this reason.
Sequel Hook: As the Autobots make their leave in order to reestablish their base on Earth, one of the Minicons that freed Megatron is shown coming out of a hatch on Kaon watching them go, showing there were survivors of the crash.
Take That!: The "Eternal Flames" Optimus was given were meant to be a Mythology Gag to the Transformers Film Series Optimus having flames, something the creative team was heavily against.*A lot of the design changes planned for Season 4 were intended to be homages to the earlier live-action Transformers film series for the sake of marketing, such as Ironhide's Earth altmode making him more resemble film-verse Ironhide, and Ratchet and Jazz having their colors changed to green and silver respectively like their film-verse counterparts. As such, Optimus wastes no time in not only calling them stupid, but also ditching them the first chance he got. TFWiki.net indicates the scene would have been cut and Optimus would have kept his flames.
Unwitting Pawn: Sentinel thinks that he has Megatron in his thrall but in truth, it's the other way around.
What Happened to the Mouse?: Or Rat in this case. Rattletrap was thrown into one of the cells on Kaon during the scuffle, but manages to sneak off right before it crashes on Dinobot Island, his whereabouts after that being unknown. Synopsis for planned episodes would have had him stranded on Earth, being hunted by Autobot and Decepticon alike, with another episode focusing on Blackarachnia adding to her army of Predacons leaving the implication Rattletrap would meet a similar fate to that of Wasp, and become Rattrap.
What the Hell, Hero?: Optimus and co. are none too pleased that Bumblebee joins Sentinel as one of the Elite Guard.
