It could be Naruto and Thor. Thor comes from a different world and has his own set of powers related to lightning and strength. Naruto also has his own unique power source in the form of chakra. They both have a warrior - like spirit. Thor would respect Naruto's power and Naruto would be in awe of Thor's god - like abilities. This mutual respect could lead to them forming an alliance first in the fanfiction.
Probably Naruto and Iron Man. Iron Man is always interested in new technology and abilities. When he sees Naruto's unique ninja abilities, especially the jutsu like Rasengan which is like a concentrated energy attack, he would be intrigued. Naruto, on the other hand, would be interested in Iron Man's high - tech gadgets. So they would start an alliance based on mutual curiosity and the potential of combining their skills.