Maybe he runs away because he's afraid for his family's safety. In fanfiction, it's possible that the Decepticons target Jack's family to get to him or the Autobots. To protect them, he decides to leave and lead the danger away from them. He thinks that by distancing himself, his loved ones will be safe.
Perhaps he runs to an abandoned military base. In the Transformers Prime world, there could be old military installations that are no longer in use. Jack might see these as a good place to hide, as they may have some remaining defenses and resources that he could use to protect himself while he figures out his next move.
One reason could be the allure of power. Unicron is an extremely powerful entity, and Jack might be attracted to that power. Maybe he feels that the Autobots' power is not enough to deal with the threats they face, and he sees Unicron as a potential solution. Another reason could be a sense of rebellion. Jack might be tired of the Autobots' rules and way of doing things, and Unicron represents a break from that.
The cool factor. Batman has a lot of cool gadgets and a mysterious persona. Jack, as a young character, might be attracted to that. He could see Batman as a role model in terms of being unique and having an edge in the fight against evil, which could translate well into his own experiences with the Autobots in the fanfiction.
Well, in such a fanfiction, perhaps Jack discovers an ancient relic that bestows upon him the power of a Prime. He then has to learn to control this newfound power while facing off against old enemies of the Autobots. Maybe he teams up with Optimus Prime and the others, using his unique human perspective to come up with strategies that the Autobots hadn't considered before.
Jack could have the power of super speed. This would let him quickly move around the battlefield, delivering important messages or distractions. It would also be cool if he could use his speed to create mini - tornadoes to disrupt the Decepticons.
She could run away because of a broken heart. Maybe she had a relationship that ended badly, and she needs to get away from the memories. In the process of running away, she could meet new people who help her heal and grow as a person. This type of storyline often explores the more vulnerable side of fem Tsuna.
One possible reason could be that he feels misunderstood by his family or friends. Maybe he has some secrets that he's afraid to share, and the fear of being judged makes him run away.
In some fanfictions, it could be that he has made a big mistake. For example, if his actions as Spider - Man led to the harm of an innocent person. He would be so guilt - ridden that he decides to run away from everything, including his friends and family in Queens.
Maybe Pikachu is feeling neglected by its trainer. If the trainer has been paying more attention to other Pokemon or is too busy with something else, Pikachu might decide to run away to get some attention.
The Decepticons would obviously be the main antagonists. Megatron would see Jack as a new threat and would try to eliminate him. Starscream might also be jealous of Jack's new status and try to undermine him in any way he can.