One way for the two worlds to merge in fanfiction is through a shared enemy. A powerful and evil force could be threatening both the Naruto universe and the Gundam Build Fighters universe. This would force the characters from both worlds to team up. The Naruto characters would bring their unique ninja abilities such as taijutsu, ninjutsu, and genjutsu, while the Gundam pilots would contribute their piloting skills and advanced technology. Together, they could fight against this common foe and in the process, learn from each other's strengths and cultures.
In fanfiction, the merge could happen because of a powerful jutsu gone wrong. This jutsu could distort space - time and connect the two universes. In the merged world, the Gundam pilots would have to deal with the threat of ninja attacks. They could use their Gundam building skills to create mechas that are better equipped to handle ninja abilities like genjutsu. Meanwhile, the Naruto characters would be fascinated by the Gundam battles and might try to participate using their own combat skills.