Two things series I'm a big fan of: the Final Fantasy series and a webcomic called Misfile.

Anyways, the idea is a time limit on Rumisiel's ability to do remote filing was finished, and thus he can not only turn the main character of Misfile, Ash, back into a boy by refiling him (its one of those genderbender comics, like Ranma 1/2 or The Wotch) but also keep anything good about his new life, such as his friendship with Emily and contact with his Mom, can be transferred. However, Rumisiel accidentally switched the papers with the disks for FF7, which were filed, and generated a second world (which due to an included reciept, anyone who had any part of the renting account's ownership was sent there). It also created a heaven interaction history with the new world, which oddly stated that a few of it's inhabitants were accidentally Misfiled.

After the Misfile(s), Cloud ended up as a girl, and Aerith is alive, with everyone's memories changed, along with reality, as if it were always so. Only the people who were Misfiled (Cloud, now known as Cirrus, and Aerith) ,the Misfile crew (given they are outsiders, they are immune), and Vincent (due to the mystical nature of his limit break demons, his memories were changed, but since all his limit break forms remembered the real events, he immediatly rejected his changed memories in favor of the ones the demons possesed_ remember the real events. The files for the FF7 world were sent to the lifestream, requiring Rumisiel to somehow access it in order to unmisfile it.

One catch: somehow, though she personally wasn't misfiled, Tifa is dead, because for one reason or another, Cloud or Aerith's misfile caused Tifa to push Aerith out of the way, getting impaled by Sephiroth instead of Aerith. I need help picking what the reason is.

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(select a group and situation to suggest, or suggest another reason why)
Scenario Group 1: Both Cloud and Aerith were Misfiled. The problem was caused by the removal of Aerith's mortuary page, which effectively reversed her death.

Situation 1A) When Aerith's mortuary page was removed, it was still calculating based on Male Cloud. Given the role of lover both Aerith and Tifa have played for Cloud, only one of them could be 'with him' at a time. When Aerith was revived, Tifa was taken instead as a way the files could assure that Cloud would only be in love with one person.

Situation 1B) Given the fact that all members of Cloud's group had to save the world multiple times, if one more hero was present, many casualties would have not happened. Therefore, Tifa was taken in Aerith's place.

Situation 1C) A critical piece of Final Fantasy 7's history was Aerith's role in summoning the lifestream manually when Holy didn't work out, as well as making the cure for Geostigma. A new person with a caring personality was needed to do this. This 'replacement' was Tifa.

Situation Group 2) Only Cloud was misfiled. Aerith only remembers because as a Cetra, she is highly spiritually aware to such a similar degree as Earth's angels, that she kept the memories of the real events regardless.

Situation 2a) Because Tifa obviously wouldn't have feelings for a female version of Cloud, she was more alert at the City of the Ancients, and was able to notice a falling Sephiroth in time.

Situation 2b) Despite the fact that it doesn't matter who would have been chosen in the game, in male-cloud's history, and the synthetic history designed to fit Cirrus in Cloud's place, different people were chosen. Male-Cloud chose a party consisting of Red XIII and Yuffie while 'Cirrus' took Tifa and Barrett.

Situation 2c) Since 'Cirrus' would have had no reason to try to impress Tifa, Tifa didn't become a guide, and thus was unceremoniously killed by Sephiroth during the Nibelheim Incident.

Situation 2d) Male Cloud's history records that he angsted over the death of two friends. Zack was still fair game, but it needed something that was of equal emotional value at the time to die to compensate for Aerith living. That person was Tifa.