Let’s start from the beginning of the last chapter. The war has ended and the party is on their way back to the Magic Academy. The “return to academy” option in the menu is disabled, so the savvy player knows something is about to go down. As soon as they get back, they find the academy half destroyed, corpses everywhere, Rem finally succumbs to her fatal disease, and a being known as the Lulusath attacking them. Also, it’s raining blood. The party then speaks to their mentor/mother figure who tells them that they have the right to decide their own fate. Defying your fate, even fate itself has almost never been mentioned prior. Maybe the fact that soldiers are reliant on commanding officers could count, but who would associate that with fate vs free will? She also reveals the nature of the Akashic Records, which has been brought up be a few NPCs: it’s states events that happened before they actually happen, similar to the Score from Tales of the Abyss, except instead of being an active force in the story, it’s never mentioned again.
They then find out that a temple has appeared, where the Arbiter will arrive. His existence has never been hinted at before. And Cid, who escaped in the previous battle, is in the temple. The party sans Rem and Machina (who left in the previous mission) follows him, and it leads to a sudden difficulty spike, in part due to the Lulusath Warriors, and the fact that you no longer have access to Eidolons or auto-heal. It’s actually legitimately challenging, coupled with foreboding music that makes it clear your chances of survival are low… then the Lulusath Warriors get an upgrade. Then it becomes cheap. Prior to that, you’re suddenly given a choice: become a l’Cie and save the world, or do so as a human. Picking l’Cie nets a sequence similar to the end of Crisis Core, in which you endlessly battle against Lulusath Warriors. Obviously, human is the right path.
You then get *sigh* a boss rush level. It isn’t too bad, as it warps you to various locations around the world to see the destruction the Lulusath Warriors have caused. You even have to fight a boss that required you to use an Eidolon before, making the fight mark the progress the characters have reached. But then you get to the Gilgamesh rematch. It’s the same fight as before, with one difference: THE FREAKIN ARENA IS CONSTANTLY BEING BOMBED. It just makes the fight unnecessarily annoying rather than difficult.
After the boss rush, you’re treated to a “climb before the hazardous liquid fills the room sequence.” For some reason, as soon as the player reaches the exit, the party is instantly killed, and warped to the next room where the party is greatly weakened. I think the intention is that they were caught in the dangerous liquid, but then why was it so easy to reach the exit?
The next room shows us a cutscene, which is a bit strange. Apparently when the party refused to become l’Cie, Rem accepted and fought the Mysterious l’Cie (who was so obviously Machina). Rem was killed, and Machina was turned to crystal shortly afterwards. You find their bodies in the room, then proceed onwards.
Then we find Cid. Turns out his body was taken over by the Arbiter, and the final boss fight begins. The party is still weakened, so it goes just as you’d expect. Then, somehow, Machina’s and Rem’s souls empower the party… because crystallized l’Cie can do that apparently, and the fight becomes easier that FFX’s final boss fight. Only difference is, FFX had Jecht to compensate for the final boss.
After the fight, the crystals are gone, magic is gone, and humanity has to make due with what they have left. The party then has a legitimately good scene. With the crystals gone, they’re now left to die just as their memories of their lost comrades come back. They come to accept it, and also discuss the fact that since the war ended, they would be free to do whatever they want. Then BUMP OF CHICKEN – Zero starts playing, and damn if it isn’t sad as hell… and then the game throws away any common sense it retained. Somehow, Machina and Rem came back to life, and discover the party’s corpses. AND THEN the game goes on to say that Machina and Rem became the leaders of the world that left the crystals behind. The problem with this is that Machina and Rem were both very clearly flawed characters; Machina let his brother’s death and his fear of losing Rem cloud his judgment into becoming a l’Cie. Rem kept her fatal illness hidden from everyone and became a l’Cie. At no point were we given any indication that they learned anything at all, and the ending goes ahead and rewards them.
The info revealed in the Codex isn’t much better. Cid’s motives regarding the war? The same as Doctor Cid from FFXII: rid the world of the crystals/gods and let humanity live for themselves. He planned to do this by first bringing about the start of the apocalypse, which is triggered by the unification of all the nations of the world. This would allow him access to the temple to challenge the Arbiter. Sorry, that doesn’t excuse him from murdering one of his own soldiers, or planning the assassination of Concordia’s queen, or the damage the world received from the Lulusath Warriors (which is exponentially higher than the damage the war brought about). The reason the party sans Machina and Rem can use magic without the crystal? Etro’s blood. Etro’s existence has not even been hinted at throughout the entire game, not even in the pages upon pages of history in the Codex. Doctor Acrecia? An entirely different goddess. Also, there are two cadets who were raised by Acrecia along with the party. Technically their existence has been foreshadowed, as the party’s names are all puns on playing cards (yes, they were the nation’s trump cards), and ten and Joker were missing. However, no info is given on what they were doing for the entire game. Nimbus? He killed himself off-screen. That last one is the worst, as he was an unbeatable plot boss earlier.
Maybe my opinion on this will change over time, but until then, uggghhh...

Like Cid, the ordinary human who thought he could kill the Arbiter by himself. Or Machina, the idiot who spent his time as a l'Cie following the crystal's orders who somehow possesses the leadership skills to lead the world after the apocalypse happened. Or Nimbus, the lvl 142 l'Cie who didn't even bother to try fight the lvl 99 Arbiter and killed himself instead.

"Ending" is misleading. "Official high school AU fanfiction" is more accurate.