A more complex plot could involve a power struggle within the Decepticons. Skywarp and Shockwave find themselves on opposite sides of the struggle, not because they have a personal vendetta against each other, but because they have different views on how the Decepticons should be led. This could lead to a series of events where they both try to outwit the other while still maintaining a certain level of respect for each other's abilities.
Maybe there's a plot where Skywarp and Shockwave are sent on a mission together. During the mission, they get stranded on a strange planet. They have to rely on each other's unique skills to survive and find a way back home. Skywarp's teleportation ability and Shockwave's scientific knowledge work in tandem to overcome various obstacles on the planet.
One plot idea could be that Skywarp discovers a hidden ability within Shockwave that not even Shockwave was aware of. This could lead to a situation where Skywarp tries to convince Shockwave to use this newfound ability for the benefit of the Decepticons, but Shockwave is hesitant as it goes against his logical programming.
You can try fanfiction websites like Archive of Our Own (AO3). There are often many talented writers who create fanfictions about Transformers G1 characters like Skywarp and Shockwave. Just search for the specific characters on the site and you'll likely find a variety of interesting stories.
One idea could be a story where Predaking and Shockwave are forced to team up against a common enemy. Maybe a new, powerful threat has emerged in the Transformers universe that neither of them can face alone. Their different skills and personalities would create an interesting dynamic as they learn to work together.
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.
A possible plot could be that Blurr is sent on a mission to stop Shockwave from activating a dangerous weapon. Blurr races to the location, but Shockwave has anticipated his arrival. They engage in a battle of wits and strength, with Blurr using his speed to dodge Shockwave's attacks and Shockwave using his advanced weaponry to keep Blurr at bay.
One common theme could be the exploration of an unlikely relationship. Skywarp has his own character traits in the Transformers Animated universe, and in Yaoi - themed fanfiction, his relationship with another character often involves themes of loyalty and devotion that go beyond the typical Transformers' relationships. Another theme might be the struggle against the norms of their own society. Since Transformers have their own hierarchies and rules, a relationship like this might face opposition, which can be a major plot point in such fanfictions.
A good plot could be that there's a power struggle within the Decepticons. Shockwave and Soundwave, who are usually on the sidelines of such politics, find themselves in the middle. They have to decide whether to side with one of the factions or stay neutral and work together to keep the Decepticons from falling apart. This would explore their loyalty and how they view the future of the Decepticon cause. Also, a plot where Soundwave's minicons are in danger and Shockwave uses his scientific knowledge to save them could be interesting. It would show a different side of Shockwave and strengthen their bond.
A simple plot could be that Jazz and Prowl are sent on a recon mission together. Jazz is excited to be out in the field, while Prowl is more focused on the task at hand. Along the way, they encounter some Decepticons. Jazz tries to outwit them with his quick thinking and charm, and Prowl uses his combat skills and strategic mind to fend them off. They return to base as heroes.
Maybe there's a crossover where a mutant has the power to control technology, and this causes a rift between the Transformers and the X - Men at first. But then they realize they need to work together to stop a greater threat, like an alien invasion that's targeting both Earth and Cybertron. The X - Men could use their powers to help the Transformers repair and upgrade in ways they never thought possible, while the Transformers provide the X - Men with powerful new weapons and defenses.
One plot idea could be that Rodimus and Ultra Magnus have to team up to face a new, powerful enemy that neither could defeat alone. Their different leadership styles - Rodimus' more impulsive and Ultra Magnus' by - the - book - could cause some initial friction but they learn to work together effectively.
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.