Well, consider a situation where Naruto's world is under threat from the Reapers. Naruto teams up with Shepard to find a way to stop them. They would have to combine their different skillsets. Naruto's ability to make friends and inspire loyalty could be used to form alliances between different species in the Mass Effect universe. And Shepard's military leadership would be crucial in organizing the ninja forces in Naruto's world.
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 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 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.
Another plot could involve a shared enemy that exists in both universes. The combined forces of Mass Effect races and Destiny Guardians have to figure out how to defeat this enemy. They would need to overcome their differences in culture and combat styles to be successful.
A great Mass Effect crossover fanfiction idea could be a crossover with the Stargate universe. The Mass Effect races could discover the Stargate network and start exploring other galaxies through it. There could be conflicts and alliances with the various races in the Stargate universe. Also, a crossover with the Dragon Age series might be interesting. The mages and warriors of Dragon Age could interact with the biotics and soldiers of Mass Effect. They could learn from each other's magic and technology, and perhaps even fight together against a dark force that threatens both universes.
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 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.
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 that the Grey Goo nanobots somehow get introduced into the Mass Effect universe and start to assimilate the technology there. For example, they might start with the Geth, who are already machines, and cause a new kind of conflict. The Reapers could also be affected, maybe the Grey Goo disrupts their harvesting cycle as it spreads uncontrollably.
Well, a really cool plot could be that the Mass Effect Relay network somehow gets connected to the Crystal Materia in Final Fantasy. This causes chaos as both universes start to blend. Characters from both sides have to figure out how to separate the two worlds again. Along the way, they discover that there are ancient forces at work in both universes that are related. Tali could use her engineering skills to help repair some of the damaged Crystal Materia, while Squall could teach her some sword - fighting techniques from his Gunblade.
Perhaps a crossover where the Covenant from Halo discovers the technology of the Milky Way species in Mass Effect Andromeda. This could lead to a power struggle as they attempt to either assimilate or destroy the new civilizations. The story could focus on how Ryder and his crew navigate this new intergalactic conflict while also trying to understand the motives of the Covenant.