One possible alternate ending could be that Iron Man and Captain America come to a truce much earlier. They realize that the real enemy is the outside force that has been manipulating them all along. So, instead of fighting each other, they join forces and expose the true villain, leading to a united Avengers once again.
If the heroes reconciled earlier in an alternate ending, it would mean a stronger Avengers. They could face future threats more effectively. For example, Thanos might not have been as successful in getting the Infinity Stones if the Avengers were united. The future of the Marvel universe would be more stable and positive.
One possible ending in the fanfiction could be that Spider - Man sacrifices himself to end the Civil War. He might put himself in a position where he has to make a great sacrifice to stop the fighting. His selfless act could be the catalyst that makes both sides see the futility of the war. Maybe he uses his powers to shield a large group of people from a powerful attack that was meant to further the divide, and in doing so, his heroism shames the warring parties into peace.
One possibility is that the shinobi skills from Naruto could be pitted against the superpowers in the Marvel world. For example, Naruto's clones might be used to confuse and outmaneuver the likes of Spider - Man. Or perhaps the Sharingan could be used to predict the moves of characters like Captain America. It would be a chaotic and exciting crossover.
One possible scenario could be that Doctor Strange saw a different future where they managed to stop Thanos before he got all the Infinity Stones. So, the Avengers might have worked together more effectively from the start. For example, they could have sent a team to intercept Thanos on his way to collect the stones on different planets.
One possible alternate ending could be that Twilight Sparkle uses her magic in a completely unexpected way to stop the wedding chaos and actually uncovers a plot that was much deeper than anyone thought, leading to a celebration of friendship rather than a wedding.
In one alternate ending, Ariel might not choose to be with Prince Eric. Instead, she realizes that her true place is in the sea with her family and friends. So she gives up on the idea of becoming human permanently and returns to her mermaid form, ruling the underwater kingdom beside her father.
One possible alternate ending could be that Anakin Skywalker resists the dark side at the last moment. Instead of becoming Darth Vader, he uses his love for Padmé to find the strength within him to reject Palpatine's temptations. This would change the entire future of the Star Wars galaxy, as there would be no Vader to enforce the Emperor's will, and the Jedi Order might be able to be rebuilt more quickly.
One possible alternate ending could be that the heroes discover a way to reverse the damage caused by Timetagger without having to fight him directly. Maybe they find an ancient artifact that has the power to reset the time changes he made. This would lead to a peaceful resolution and the restoration of the original timeline.
In a different take for an alternate ending, the Phantom could expose his face to the public in a grand gesture. He shows that despite his disfigurement, he is a man of great talent and feeling. The public, moved by his music and his courage, accepts him. Christine then falls in love with the new - confident and accepted - Phantom, and they build a life together where the Phantom becomes a respected figure in the Parisian art scene.
One possible alternate ending could be that Doctor Strange actually manages to defeat Thanos using his magic before he can snap his fingers. Strange could have found a way to trap Thanos in a time loop or a different dimension, thus preventing the mass destruction that occurred in the original ending.