Continued
>>95331103Season 3 would be the aftermath of the season 2 final, where most of the main bot and con cast is scattered in space, and basically have space adventures eventually making their way back to Earth only for after a few months of being gone, Devastator has been fully realized and now takes over the Earth. So this is kinda like a DOTM/All Hail Megatron end of the world invasion plotline.
Season 4. Megatron eventually discovers a new mcguffin at the end of the 3rd season and leaves Earth to go and revive Cybertron. Optimus leaves too, to go after Megatron, leaving the rebuilding Earth in the hands of Hot Rod (who now calls himself Rodimus) and Prowl and their leadership styles buttheads the entire team, Starscream returns with his own crew. Optimus also reunites with his old comrade Ironhide and flame Elita-1 in his journey to Cybertron. Also we see the Decepticon high command currently lead by Overlord take an interest in Megatron's scheme, eventually becoming a 3 way fight between Optimus, Megatron and Overlord. Also Harold Attinger becomes the human villain trying to outlaw the Transformers after what happened in the previous season.
Season 5, the time skip season and the final season. Unicron shows up, Megatron is rebuilt into Galvatron, Optimus finally becomes leader of the Autobots after bringing Cybertron back to life, Rodimus along with the newly retired Ultra Magnus travel in space on the Lost Light having shenanigans (eventually tying into the Unicron plot), also Spike and Carly finally settle down with Daniel but their happy life might be challenged by newcomer villain Dylan Gould and his goons Hydra & Buster (Darkwing and Dreadwind), eventually this leads to an epic finale.
I'd also have an OVA going on in this continuity following other characters like Devcon in their travels across the galaxy.