One idea could be Shepard accidentally getting thrown into a dimension where the Reapers are already victorious. They have to find a way to team up with the remnants of different species to reverse the situation. Another could be a dimension where the Mass Effect fields work differently, leading to unique biotic and tech abilities that Shepard has to learn to use in order to get back home.
A cool plot might be that a character discovers a dimension where the Protheans never died out. The story could then explore how they interact with the Protheans and how this new knowledge can be used to prevent the Reaper threat in their own dimension. Also, a dimension where all species are merged into one super - species due to some strange dimensional anomaly could be an interesting setting for a fanfiction.
One idea could be having the XCOM soldiers use their combat skills in the Mass Effect universe. Maybe they are sent to help fight against the Reapers. They could introduce their unique tactics and weaponry to the Mass Effect races.
One idea could be that Naruto is somehow transported to the Mass Effect universe and his unique abilities draw the attention of various female characters. They see his determination and power as something new and exciting, leading to a harem situation. For example, characters like Liara might be intrigued by his chakra abilities which are completely different from biotics in their world.
One idea could be exploring the political intrigue within the Terran Empire. How different factions vie for power and influence. Another could be the discovery of a new alien species by the Empire and how they handle it, whether through diplomacy or force.
A possible plot is that the OC's amnesia is caused by a powerful biotic attack. As they try to regain their memory, they discover that they have unique biotic abilities that they didn't know about before. They could then be recruited by Cerberus, thinking they are on the side of good, but as they start to remember more, they realize Cerberus's true motives. They might also have a connection to an ancient asari artifact that holds the key to both their past and the future of the galaxy, and different factions are vying for control of it.
One idea could be that Naruto, with his unique abilities like the Rasengan and shadow clones, gets transported to the Mass Effect Andromeda universe. He could use his ninja skills to help the Pathfinder team in combat situations against the Kett or other enemies.
One idea could be the integration of the mobile suit technology from Gundam into the Mass Effect universe. For example, Shepard's team could discover a lost Gundam unit and try to figure out how to use it against the Reapers. Maybe the advanced beam weaponry of the Gundam could be a game - changer in the fight.
A plot could revolve around a human scientist in an independent colony who discovers a way to enhance biotic abilities without the use of the traditional Mass Effect implants. This causes a stir among the different factions, both human and alien, as it could change the balance of power. Some see it as a great opportunity for humanity to stand on its own, while others fear it will bring unwanted attention and conflict.
A possible plot is that a Mass Effect technology is introduced to the Naruto universe. Maybe a Mass Relay is found in the Hidden Leaf Village. This could lead to a whole new set of adventures as the ninja try to figure out what this strange technology is and how it can be used. Or, characters from both universes could be combined. Like a Turian with Sharingan abilities.
One idea could be that Venom's symbiotic nature interacts with the biotics in the Mass Effect universe. Maybe the symbiote gives a character enhanced biotic abilities that are unique and unheard of. For example, instead of just pushing or pulling with biotics, they can create a sort of living shield made of the symbiote's substance.
One idea could be that Naruto is somehow transported to the Mass Effect universe. He could use his ninja skills, like his shadow clones, in combat against the various alien species in Mass Effect. Maybe he teams up with Shepard and they learn from each other's combat styles.