Another option for the main villain in a Naruto banished Mass Effect fanfiction could be a power - hungry Spectre. This character could be jealous of Naruto's abilities and popularity among the different species. He'd use his position and resources to frame Naruto and turn the various races against him, all while he secretly plots to gain more power and control in the galaxy.
Well, in a Naruto banished Mass Effect fanfiction, the story could start with Naruto being wrongly accused in his world and sent away. Once in the Mass Effect setting, he could form alliances with different species. For example, he could team up with the Turians due to their military discipline which might remind him of the shinobi way. His jutsu could also be a source of great mystery and power in that universe, leading to various adventures as different factions either try to recruit him or eliminate him.
It could be Shao Kahn. Since Naruto is an outsider in the Mortal Kombat world, Shao Kahn might see him as a threat or just a toy to play with. He could be the one who wants to either kill Naruto or use his power for his own evil plans.
Danzo might be the main villain. He's known for his underhanded tactics. He could have banished Naruto to create chaos and then sent his Root agents to destroy Konoga for some political or power - related reasons. He might see Konoga as a threat to his control over the village in some way.
The main characters are Naruto and Jack, but the fanfiction could also introduce new characters that are a blend of the two universes. For example, there could be a character who has both chakra - like Naruto - and biotic abilities - like Jack. This new character could be the result of some experiment gone wrong or a natural occurrence in the combined universe of the fanfiction. And of course, there would be various antagonists, such as the usual bad guys from the Mass Effect universe who see Naruto as an unknown and dangerous variable, and perhaps some of Naruto's enemies from his own world who have also found their way into the Mass Effect universe.
Shepard could be a main character. Given their experience in uniting different species and facing great threats, they would be a natural fit in a world war scenario. They could lead a coalition against a new enemy.
Shepard from Mass Effect could be a main character. They could lead the XCOM forces in a joint mission against a common enemy. Their leadership skills would be very useful in coordinating the two very different groups.
Shepard could be one of the main characters. Imagine Shepard having to deal with Venom's presence. Shepard's leadership skills would be put to the test as they try to figure out if Venom is a threat or an ally. Also, Garrus could be involved. His combat skills and loyalty to Shepard would make for some interesting interactions with Venom.
Liara T'Soni would be a great candidate. She is intelligent and curious, and Naruto's different abilities and his unique personality would likely draw her in. She would be interested in studying his chakra and his ninja techniques.
Well, one way it could work is if the Naruto scientist was brought into the Mass Effect universe through some sort of inter - dimensional rift. Maybe they could use their ninja knowledge of chakra and apply it to biotics in the Mass Effect world. For example, they might find similarities between how chakra is controlled and how biotics are manipulated.
An Asari scientist could be a main character. She might be intrigued by the mystery of the abandoned Earth. Her knowledge of biotics and different cultures in the Mass Effect universe could help her in deciphering the secrets of Earth. She could be the one to make the first contact with any remaining humans or discover important artifacts. Also, a Krogan mercenary could be a main character. His brute strength and combat skills would be useful in exploring the dangerous and desolate Earth. He might be in it for the loot or just the thrill of adventure.