If I had to pick one, I would say
Megalith Agnus Dei. The song is absolutely beautiful, a mixture of symphonic, choral, and electronic music. During the fight it plays in, you can hear, over the radio, several characters dying in real time to buy you time. The song's lyrics, taken from liturgical hymns, translate to "Lamb of God, who takes away the sin of the world, give them rest, and let eternal light shine upon them."
Following that, a few runners up...
Bergentrücking/Asgore is a wonderful composition. Very few songs manage to carry the weight of a final battle against a sympathetic character, but this one nails it. It's determined (quite fitting with the theme of the game), yet sorrowful, looking back even as it marches forward. It ties in several motifs, including Determination, Asgore's theme, and Toriel's theme, hinting at several plot elements that hadn't yet been explained. It's the perfect note to end the game on.
Unfortunately, the game didn't understand this and didn't have the courtesy of actually ending here.
The Light That Burns The Sky is another song that makes good use of motifs, combining Nebby's theme with Necrozma's, then trying in the Ultra Space and final dungeon themes for good measure. And then playing them on a rock organ. Because rock organs make everything better. I tend to be a fan of the more "encouraging" final boss themes, so to speak, and this one plays to that wonderfully.
The Key We've Lost almost feels like cheating, since Sawano, outside of this game, composes only anime music. But that's why the song is great. In his usual style, it's a fusion of orchestral and electronic elements, with Mika Kobayashi belting out semi-connected lyrics in somewhat broken English over the song's latter half.
The Unsung War is how I'm wrapping out this list, cuz Ace Combat deserves at least two mentions. Compared to the game's penultimate mission, the final boss is smaller in scope and quieter, and the music compliments this. The lyrics relate the tale of Razgriz, a fictional demon who the protagonists of the game are frequently compared to. Much like their own story, the song begins humbly before gradually building into something quite incredible. The song also ties in the motif of another character, the last member of the squadron who died earlier in the game while an
equally beautiful song played.