There could be a story about a female Decepticon who discovers a powerful ancient artifact. The other Decepticons and Autobots then race to either get the artifact from her or convince her to use it for their side. This would lead to battles, alliances, and betrayals as everyone tries to gain the upper hand with the power of the artifact.
Imagine a female Decepticon who was once an Autobot but was brainwashed by the Decepticons. She slowly starts to regain her memories and has to fight against her programmed Decepticon self. She could be a key to bringing peace between the two factions if she can fully break free from the Decepticon control. This would involve her facing many challenges and making difficult decisions.
There could be a fanfiction where a powerful female Decepticon discovers a long - lost power within herself. This new power makes her a target among both the Decepticons and the Autobots. She has to decide whether to use it for good or evil while also fending off those who want to control her for their own purposes.
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 common theme is the power struggle. Since the Decepticons are known for their desire for power, when a human is involved, it often becomes a central point. For example, a human might get caught in the middle of the Decepticons' fight for dominance.
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 idea could be that Jack discovers a hidden power within Arcee that she was not aware of herself. They then have to go on a quest to find out more about this power and how it can be used to help the Autobots in their fight against the Decepticons. Another plot could be that Jack gets lost in a dangerous part of Cybertron and Arcee has to brave all sorts of perils to find and rescue him.
Perhaps there is a portal that connects Cybertron and Equestria. Some ponies accidentally end up on Cybertron and are shocked by the mechanical world. The Transformers have to help them get back home. Meanwhile, some Autobots are curious about the ponies' world and decide to accompany them. This leads to a cultural exchange of sorts between the two groups, with lots of misunderstandings at first but then growing respect and friendship.
A plot could revolve around the baby Dinobots befriending a group of small, local Cybertronian creatures. These creatures are being threatened by a natural disaster on Cybertron. The baby Dinobots, with their unique skills and courage, decide to help the creatures survive the disaster, all while learning valuable lessons about friendship and responsibility.
A plot could involve Bumblebee getting damaged and losing his memory. The RWBY characters find him and try to repair him while also helping him regain his memories. As they do this, they learn about the Transformers universe and Bumblebee starts to adapt to the RWBY world, eventually using his unique abilities to help them in a big battle against a powerful Grimm horde and a new villain that has emerged.
A cool plot idea could be that the Transformers are mistaken for a new type of Sith - created abomination. The Jedi initially try to destroy them, but then realize they are something different. Another idea is that a Transformer becomes a Jedi Knight, using its unique abilities in combat and its own code of honor which is similar to the Jedi Code.