Another plot could revolve around a Rogue Trader facing a mutiny on their ship. Maybe the crew has been influenced by a chaos cult or they simply disagree with the Trader's latest high - risk venture. The Trader has to find a way to regain control and deal with the traitors.
A more complex plot could involve a Rogue Trader getting caught in the middle of a political power struggle between different factions in the Imperium. They are used as a pawn by some powerful lords, but they also see an opportunity to gain more power and influence for themselves if they play their cards right. This would involve a lot of political intrigue, back - stabbing, and difficult decisions on the part of the Rogue Trader.
One popular character is Captain Elias Hawkwood. He is often depicted as a fearless Rogue Trader who has a reputation for always coming out on top in the most dangerous situations. His ship, the 'Starlight's Bane', is also well - known in many fanfictions.
One idea could be a vampire Space Marine. Maybe a genetic experiment gone wrong in the Imperium that results in a Marine with vampiric traits. He has to struggle with his newfound thirst while still trying to fulfill his duty to the Emperor.
A really interesting plot could revolve around the origin of the demons in both universes. The fanfiction could explore if there is a connection between the Chaos demons in Warhammer 40K and the demons in Doom. Maybe the Doom Slayer and a Warhammer 40K Inquisitor work together to uncover this mystery while fending off the never - ending waves of enemies.
One interesting idea could be the combination of Naruto's ninja abilities with the high - tech and grimdark elements of Warhammer 40k. For example, Naruto's shadow clone jutsu might be used in a unique way on the battlefields of the 41st millennium. Maybe the clones could be used to infiltrate enemy lines or to overwhelm ork mobs.
Perhaps a Dark Eldar wych could form an unlikely alliance with a Space Marine. Maybe the wych has a personal vendetta against a chaos warband that is also targeting the Space Marine's chapter, and they decide to work together to take down the common enemy. This would involve a lot of tense moments as they try to trust each other despite their very different cultures and motives.
Perhaps an Imperial Inquisitor ends up in the Star Wars galaxy and tries to manipulate the Sith and Jedi for his own ends. He could see the Sith as a useful tool, not realizing how dangerous they truly are until it's almost too late. This could lead to a three - way battle between the Inquisitor, the Sith, and the Jedi.
One interesting Rogue Trader fanfiction could be about a young and inexperienced Rogue Trader who discovers a long - lost alien technology on a desolate planet. This technology has the power to either save or doom the galaxy. Another might focus on the political intrigue within the Rogue Trader dynasties, like a power struggle between different branches of a family for control of their vast fleets.
One idea could be a crossover with the Star Trek universe. The Tyranids could be seen as an extremely hostile alien force that the Federation has to deal with. Their bio - ships and swarming tactics would be a huge contrast to the more technological - based Starfleet.
One idea could be inserting yourself as a new recruit in a Space Marine chapter. You could experience the brutal training and the strict code of honor. Another is to be a tech - priest, exploring the complex machinery and the religious aspects tied to it. Maybe even be a rogue trader, traveling the galaxy in search of profit and adventure.
Another interesting concept is to have a Primarch face a completely new enemy. Not the usual chaos forces or xenos, but something from within the Imperium itself that has turned against it. This would create a lot of internal conflict and moral dilemmas for the Primarch to deal with.