One idea could be that Optimus Prime travels back in time to prevent the creation of a powerful Decepticon weapon. This would change the whole course of the war. Another could be a human character traveling to the future of the Transformers' world to see how the conflict ends and bring back knowledge to change the present situation. And perhaps a Decepticon time - travels to the past to rewrite history and make themselves the rulers from the very beginning.
Well, a cool plot might be where the Autobots and Decepticons accidentally get sent to different time periods due to a malfunctioning space - bridge. The Autobots end up in a pre - war Cybertron and have to try not to disrupt the timeline while finding a way back. The Decepticons could land in a time when humans first discover Cybertronian technology and try to take over the Earth much earlier. Also, a character could time - travel to save a fallen comrade who died in a previous battle, changing the relationships within the group.
Here's a plot. A time - traveling device is discovered on Earth by the Autobots. They realize it was left behind by an ancient Cybertronian explorer. Some of the Autobots decide to use it to go back in time to find out more about their origin. But the Decepticons get wind of it and also send some of their troops. Once in the past, they all have to deal with the different environment, meet their ancestors, and face the challenges of not changing the timeline too much while still achieving their goals.
One plot idea could be Megatron traveling back in time to the very beginning of the Cybertronian war. He could try to change the initial strategies that led to his early defeats, using his knowledge of future events. Maybe he'd attempt to eliminate Optimus Prime before he becomes a major threat.
Jack could travel to a time when the Autobots first arrived on Earth and help them understand human culture faster, thus forging stronger alliances earlier. This would change the whole dynamic of the war on Earth.
One idea could be a story where Optimus Prime has to team up with an unlikely ally from another planet. Maybe a small, scrappy alien that has some unique abilities that can help in the fight against the Decepticons. This would add an interesting dynamic as Optimus has to learn to work with a very different being.
A plot idea could be that Optimus Prime time - travels. He goes back to the beginning of the war between the Autobots and the Decepticons and tries to prevent it from starting. Along the way, he meets younger versions of his friends and enemies and has to deal with the consequences of changing the past. Or perhaps, Optimus is trapped in a dimension where the laws of physics are different. He has to adapt quickly and find a way back to his own world while also facing off against new threats.
One plot idea could be that Female Optimus Prime has to lead a team of misfit Autobots to save a planet from a new, powerful Decepticon threat. She has to use her unique leadership skills and strength to unite the team.
One idea could be exploring Starscream's origin as a 'baby' in the context of the Transformers Prime universe. Maybe he was created with a special purpose that was later forgotten or corrupted.
There could be a fanfiction where Bumblebee loses his memory. Arcee takes it upon herself to help him regain it. She takes him to all the places they've been together, shares their memories, and tries to jog his memory. As she does this, she also realizes how much Bumblebee means to her and how important their relationship is. This is a story about friendship, loyalty, and the power of memories.
One idea could be an OC who is a medic that gets captured by Megatron. Megatron initially sees the OC as a tool to use against the Autobots but gradually develops an odd respect for the OC's skills and tenacity. Another plot could involve an OC who has a special power that Megatron wants to harness for his own evil plans. As he tries to manipulate the OC, the OC starts to see through his lies and tries to turn the tables on him. A third plot might be an OC from a different dimension who accidentally lands in the Transformers Prime universe and catches Megatron's attention. He's intrigued by this strange new being and tries to either recruit or destroy the OC.
Perhaps a fanfiction where Soundwave gets damaged in a fight and Megatron has to make a difficult decision about whether to risk everything to save him. It could explore their loyalty to each other. Or a plot where they are betrayed by one of their own and they have to work together to expose the traitor.
A great plot could be that a powerful artifact from the Transformers universe is found on Earth and it has the power to either save or destroy the planet. The Avengers initially think it's a new weapon or power source, while the Autobots know its true origin. They have to convince the Avengers of its importance and together protect it from the Decepticons and any other villains who want to use it for their own evil purposes.