One possible alternate ending could be that the main characters manage to find a hidden, untouched area where the virus has not spread. They start a new community there and figure out a way to immunize themselves against the virus using local plants or something unique to that area.
Perhaps in the fanfic's alternate ending, the infected somehow regain their humanity. It starts with a few of the less severely infected showing signs of recognition. Eventually, they are able to communicate and help the remaining humans find a way to reverse the virus completely. This would be a very different and more positive take on the '28 Weeks Later' story.
In an alternate ending, the military could have actually been successful in containing the virus. They develop a cure using the antibodies of those who were initially immune. The remaining survivors are then able to rebuild society much faster than expected. They use the knowledge of the virus outbreak to create better safeguards for the future.
If the alternate ending was a happy one where everyone was cured, the overall tone would change from dark and apocalyptic to hopeful and optimistic. It would be a complete shift from the sense of doom that pervades the original story.
Let's say in the original story, the cupcakes were made to bring two estranged friends back together. In the alternate ending, the cupcakes get ruined on the way to the meeting place. But this misfortune makes the two friends realize that their relationship was never about the cupcakes. They end up reconciling in a more profound way, understanding that it was their shared memories and mutual care that really mattered. So, the cupcakes, though not present physically, still played a role in their reunion by their absence.
One possible alternate ending could be that Jafar actually manages to outwit Aladdin in the final battle. Instead of Aladdin winning and getting the girl and the kingdom, Jafar takes over completely. He turns the kingdom into a dark and desolate place, with all the citizens living in fear. Aladdin is banished to the desert, and Jasmine is forced to be Jafar's prisoner. This would be a much darker and unexpected ending compared to the original.
Another alternate ending could be that there is a big battle between the living and the dead. Victor manages to broker a peace treaty between the two worlds. As part of this, the Corpse Bride is given a special place in the living world. She becomes a sort of guardian between the two realms, and Victor stays with her as her companion, and they both ensure that the living and the dead co - exist peacefully.
In an alternate ending in fanfic, the spell could have been broken in a different way. What if instead of Belle's declaration of love, it was the Beast's selfless act towards the villagers that broke the spell? For example, when the villagers come to attack the castle in fear, the Beast could have chosen not to fight back and instead protect them from some other danger. This act of kindness and selflessness could have been the key to breaking the spell, and he turns back into a prince. Belle then realizes she has fallen in love with him not just for his new form but for his noble heart.
Well, imagine if Romeo didn't believe the false news of Juliet's death at all. He decides to go and rescue her from the tomb instead of killing himself. When he arrives, Paris is there, but Romeo manages to defeat him without killing him. Then, he wakes Juliet up, and together they run away to a far - off land where no one can find them, leaving their families behind to deal with the consequences of their feud.
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.
Maybe the couple could decide to part ways and pursue their individual dreams instead of staying together. That would be a surprising and unconventional ending.
There could be a fanfiction that delves into the backstories of the infected. Maybe it shows how they were normal people before and what led them to become the terrifying creatures. This would add more depth to the whole '28 Weeks Later' universe.