Philemon more or less rewound time before the events and placed the party in a time frame where IS didn't actually happen, thus creating a different timeline not too different from Zelda OoT where there is the timeline where Link becomes an adult and saves the world and one where he prevents the events from ever happening when he was a child.
I wouldn't say it really cheapened their sacrifice since they basically sacrificed their friendship to save the world by creating a new timeline. It's made more tragic when you realize P2:EP Ending spoilers Other Side Tatsuya had to sacrifice ever being with his friends again by returning to the Other Side to prevent Nyalarthotep from screwing with the new timeline since it's his own memories that allow the two alternate realities to merge in the first place. It's implied that his friends don't exist in the Other Side anymore so Tatsuya will be alone. The Lisa, Jun, and Eikichi in EP are very much the ones from IS whereas the Tatsuya of This Side is now an alternate one who really never did meet the others. This ending can be even more tragic if you allow the IS team to remember the Other Side though it also makes the final boss significantly more difficult.
Honestly, I feel like it was a clever and interesting premise, like Chrono Cross but slightly less preachy and a better cast and battle system.





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