In the ending credits Post-"And thus Boy met Girl", we witness Pneuma's core crystal reactivating in Rex's hand. The core crystal had remained intact in spite of Pneuma's
Heroic Sacrifice, and later reintroduces Pyra and Mythra as separate entities in front of everyone while voyaging toward the new land. Some people cite this moment as an
Ass Pull, but there's justification for their resurrection despite what had happened at the Orbital Ring.
From Chapter 3 and onward, we've been treated to Mythra and the nature of Pyra as a coping-mechanism for the tragedy that happened 500 years ago on Alrest. It's never stated what Pyra is to Mythra, but she fits the dictionary definition of a
Tulpa. In Layman's Terms, he's an aspect of Mythra made independent from her, and Mythra in turn ends up being Pneuma's Tulpa as well. A recursive Thoughtform, if you will.
Being an Aegis, Pneuma can tap into the entire library of Blades and relay information, presumably revert/accelerate a Titan's age, manipulate all elements, shorten Rex's anchor so it conveniently falls to the bottom of the port bridge, and travel FTL (at least within the game's context). Combine those feats with her
god-like abilities and it's not unreasonable to assume that she created Mythra and Pyra the same way Klaus had the Cloud Sea form the earliest Core Crystals from all of the nano-binding.
So where does Pneuma's sacrifice and Pyra and Mythra's recovery fall here? It's simple:
Pneuma died, but Pyra and Mythra are independent Beings whose minds come together to form Pneuma's body. After Pneuma had discarded her physical form controlling the last of Aion's power, she channeled her remaining life force back into her Tulpas while permanently discarding away her true form. Now that Pyra and Mythra
exist separately, they act as the remnants of Pneuma, with the newly-formed land ahead of them, Rex, Poppi and the rest of their friends, and the Phoenix symbolism with the Blades and Titans coming full circle.