Perhaps a plot twist where Naruto, using his chakra, is able to disrupt the mass effect fields in a way that no one expected. This causes chaos in the Mass Effect universe, but also reveals a hidden potential in the combination of the two different power systems. Fem Shepard has to rely on Naruto's knowledge of chakra to fix the problem, and in the process, they form a much deeper bond. It also changes the way the characters in the Mass Effect universe view the Naruto universe's power systems.
One interesting plot twist could be that Fem Shepard is actually related to a powerful clan in the Naruto universe. This could be revealed through some sort of genetic discovery. It would completely change her understanding of herself and her place in both universes. Another twist could be that Naruto discovers he has latent biotic abilities that are only awakened when he is in the Mass Effect universe. This would give him a whole new set of powers to explore and master, and also create a connection between him and the technology - based world of Mass Effect.
One possible plot could be that Shepard's ship somehow gets teleported or stranded in the Naruto universe. She meets Gaara, and at first, they are both cautious. But as they start to understand each other's powers and motives, they form an alliance. Maybe they have to fight a common enemy that is threatening both their worlds. For example, a new type of Reaper - like entity that is also interested in the chakra in the Naruto world.
One interesting plot twist could be the combination of Mass Effect's biotics with Warhammer's psychic powers. Imagine a character who has both and has to learn to control this new, extremely powerful force. It could lead to a situation where they are feared and hunted by both sides of the crossover world.
One interesting plot twist could be the combination of Stargate's wormhole technology with Mass Effect's mass relays. Imagine if the two were somehow integrated, allowing for new travel routes across galaxies. Another could be characters from the two universes swapping abilities. For example, a Mass Effect character getting access to Stargate's Ancient technology and using it in unexpected ways.
Another possibility is that Naruto is transported to the Mass Effect universe. He would be a very unique character there. His ability to never give up and his strong sense of justice would fit well in the often morally - grey world of Mass Effect. He could use his ninja skills, such as his shadow clone jutsu, in combat situations in the Mass Effect universe. This would be quite a spectacle for the other characters, like Fem Shepard. She might initially be skeptical of Naruto's abilities but come to respect him as they fight together against common enemies, like the Reapers.
A great plot twist might be that the Reapers from Mass Effect somehow end up in the Gears of War world. The Locust could initially see them as allies against the humans, but then the Reapers turn on them as well. It would create a chaotic situation where the Gears of War characters have to team up with some of the Mass Effect races they previously didn't trust to fight a common enemy that is far more powerful than anything they've faced before.
In some fanfics, a plot twist could be that a Harry Potter character is actually a long - lost descendant of a powerful Sith. This completely changes the way they view their own magical abilities and heritage. Another interesting twist could be Mass Effect technology being introduced into the Harry Potter world, like biotic powers being mistaken for a new type of magic. It flips the normal understanding of both universes on its head.
One interesting plot twist could be the combination of Call of Duty's military tactics with Mass Effect's alien races. For example, imagine soldiers from Call of Duty having to fight alongside the Krogan in a battle against a new, powerful enemy that has elements of both universes. Another could be the use of Mass Effect's biotics in a Call of Duty - like urban warfare setting. This would completely change the dynamics of combat as we know it in the Call of Duty world. And perhaps a plot twist where a character from one universe gets transferred into the other and has to adapt to a completely different set of rules and technologies.
Shepard and Tali's relationship in fanfiction can also take a more romantic turn. Writers might describe their growing feelings for each other, starting from their initial meetings and gradually developing into a deep love. This could involve tender moments between them, like sharing a quiet moment on the Normandy while looking out at the stars, and how they overcome the differences in their species and cultures to be together.
One possible plot could be that Shepard and Tali decide to face the challenges of pregnancy together. They might have to deal with the reactions of their friends and comrades. For example, Garrus could be initially shocked but then offer his support. Tali would have to adapt to the physical changes while still being an important part of the team. Shepard, on the other hand, would be protective and ensure Tali's safety during missions. Maybe they would also start thinking about a more stable future, like finding a place to settle down away from the constant chaos of war.
The character development of the fem Harry Potter is also fascinating. Since she is in a completely different universe, she has to grow and change. She might start off being naive about the ways of the Mass Effect world but then quickly learn to adapt and use her skills to her advantage. Also, her relationships with the characters from Mass Effect, whether it's a friendship or a rivalry, add depth to the story.