Well, Ben is obviously one of the main characters as the story is centered around him and the Omnitrix. Gwen might also be a main character as she often plays an important role in Ben's adventures, providing support or using her own magical abilities to help out. Grandpa Max could be another main character, offering his wisdom and experience to guide Ben through various situations.
One interesting storyline could be about Ben exploring new alien forms that were previously unknown in the official series. Maybe he discovers a form that has unique powers that he has to learn to control quickly to face a new and powerful enemy.
One idea could be that Ben discovers a new and powerful alien form in the Omnitrix that has abilities he's never seen before. He has to quickly learn to control it to defeat a new and dangerous villain.
One possibility is that the story could explore how Gwen's personality changes when she has the Omnitrix. She might become more confident or more responsible. Also, there could be new villains who are attracted to the Omnitrix now that Gwen has it. She would then have to face these threats and protect the Omnitrix from falling into the wrong hands.
In this fanfic, the relationships among the Omnitrix aliens - as - humans would be full of surprises. The competitive relationships between some aliens might turn into friendly rivalries. Take Diamondhead and Four Arms, for instance. As humans, they might compete in sports rather than in battles. Their relationships with humans who don't know their true identities would also be interesting. They would have to constantly lie to maintain their cover, which could lead to feelings of guilt and isolation. But at the same time, they could form deep and meaningful relationships with those who accept them for who they are, despite their secrets. This would create a web of relationships that are both complicated and fascinating to explore.
The story could start with Gwen unexpectedly getting the Omnitrix. Then, she might start exploring the different alien forms she can transform into. She'd likely test out their powers in various situations, gradually getting a handle on how to use them effectively.
Perhaps a plot where the human - like aliens are being hunted by an evil organization that wants to study and use their powers. They have to rely on their wits and the help of a few trusted humans. Diamondhead as a human could use his crystal - like skin ability in creative ways to defend against the hunters. And they could also start to question whether they are more alien or more human as they fight for their freedom, which would be a great exploration of identity in the context of this fanfic.
Gwen would be a great character to pair with Alien X. Her magical abilities could complement Alien X's powers in interesting ways. For instance, when facing a threat that requires both brute omnipotent force and the finesse of magic. Another good pairing could be Kevin. His ability to absorb and use different forms of energy could interact with Alien X's power source in unexpected ways, like when they need to combine their powers to break through a powerful energy barrier.
One common theme is friendship. The female alien often forms a strong bond with Ben, and they support each other through different situations. Another theme is power. The female alien usually has some unique power that plays an important role in the story.
I'm not entirely sure about the exact plot details of 'ben 10 ultimate alien the big story'. It might involve Ben Tennyson using his various alien forms to face some big threats and challenges, but that's just a general guess.