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 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.
In a time travel fanfiction about Jack from Transformers Prime, he might accidentally be sent to a future where the Autobots have either won or lost the war in extreme ways. If they won, he could see a utopian Cybertronian - human coexistence. If they lost, he'd have to find a way to go back and change the past to prevent such a dark future.
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.
One idea could be to write about how the other Autobots react to Jack being hurt. For example, Arcee might become extremely protective and vow to find whoever or whatever caused the harm. She could go on a solo mission to seek revenge while the other Autobots try to keep Jack stable and safe at their base.
The OC could be from another planet that has a connection to Cybertron. Jack and the OC meet when she is looking for something on Earth related to her home planet. They start off as strangers but gradually fall in love as they discover more about each other's worlds.
One plot idea could be Jack and Miko getting lost in an uncharted part of Cybertron. They have to rely on each other's skills, Jack's strategic thinking and Miko's boldness, to find their way back. Another could be a situation where they accidentally switch bodies due to some alien technology malfunction. This would lead to humorous and also challenging situations as they try to adapt to each other's lives while in the wrong bodies.
One idea could be that the Autobots immediately launch a rescue mission. They use their advanced tracking systems to find Jack. Maybe Ratchet has some new tech that can detect Jack's unique human energy signature. They face many challenges on the way, like Decepticon traps.
One plot idea could be that Jack discovers his new wings in a moment of danger. Maybe during a battle against the Decepticons, some sort of energy surge activates a latent ability in him and the wings suddenly sprout. This new ability gives him an edge in combat, allowing him to fly and perform aerial maneuvers that catch the enemies off - guard.
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.