One interesting plot twist could be that Danny's ultimate enemy turns out to be a future version of himself who was corrupted by too much power. Another might be that the enemy is actually someone he thought was a friend all along, but was secretly plotting against him. And sometimes, the ultimate enemy is an alternate version of Danny from a parallel dimension where he made different choices and became evil.
One idea could be exploring what would happen if Danny made a different choice during his encounter with the ultimate enemy. For example, if he tried to reason with his enemy instead of fighting right away.
One interesting plot twist could be that the accident was actually caused by a future version of Danny trying to change the past, but in doing so, made things worse. So when present - day Danny has the accident, he starts to notice strange things that lead him to suspect time - travel interference.
One interesting plot twist could be that Danny's friends initially don't recognize him as Dan Phantom and try to befriend him, not realizing the danger. Another could be that Dan Phantom has some hidden memories of his time as Danny that start to resurface at crucial moments, changing his evil intentions.
Sam and Tucker are also great characters to include. They are Danny's best friends and can provide support, comic relief, or get into trouble themselves, adding more layers to the fanfiction.
The most common characters in Danny Phantom Ultimate Enemy fanfiction are Danny, of course. He's the main character so he's always there. Vlad is another one. He has so much potential as an antagonist. Sam and Tucker are also popular as they are Danny's support system. Additionally, some of the more powerful ghost villains like Pariah Dark also make appearances. They add more danger and drama to the stories as they are extremely powerful foes that Danny has to face. Plus, Danny's parents sometimes play important roles as well, especially when their inventions or their knowledge of the ghost world get involved in the plot.
A cool plot twist could be that the pregnancy is a sign of Danny's evolution into a new form. Instead of it being a normal biological pregnancy, it's a supernatural transformation. As he progresses through the 'pregnancy', he gains new powers and abilities that he has to learn to control, and in the end, he emerges as a more powerful version of himself.
Maybe Dani is not really Danny's clone in the way they thought. There could be some other mysterious force or entity that had a hand in her creation, and as they dig deeper into her origin, they find out that she has a much greater destiny than just being Danny's 'daughter' in a sense. This would completely change the dynamic of their relationship and the direction of the story.
A great plot twist could be that Ember was actually working undercover for a greater good all along. Everyone thought she was a villain, but she was trying to stop an even bigger threat from the Ghost Zone. Danny finds out about this when he accidentally stumbles upon her real mission.
A great plot twist could be that one of the Robin Brothers turns out to have a secret connection to the ghost world. Maybe he has a long - lost relative who was a powerful ghost and this connection is revealed during a battle against a major ghost villain. This would completely change the dynamics of the team - up and add a new layer of mystery.
A common plot twist is when Sam gets a new power or ability that Danny didn't know about. For example, she might be able to communicate with a certain type of ghost that holds the key to their relationship. This throws Danny off guard and adds a new dynamic to their love story.