[Major spoiler ahead]

Genesis died in Crisis Core:

The Lifestream. That's what we call the river of life that circles our planet, giving life to the world and everything in it.
—Marlene, in the prologue to Advent Children

The scene when Zack defeats Genesis (the last battle ) and got thrown into the Lifestream.. he >died actually< then a moment later granted life back (when he got rejected by the goddess ) falling into a coma immediately right after "getting kicked" outta the Lifestream....what or who saved Genesis then if not the Goddess?

Even if the morrow is barren of promises
Nothing shall forestall my return
To become the dew that quenches the land
To spare the sands, the seas, the skies
I offer thee this silent sacrifice

Another take: Genesis to Zack "We will all ...Join the lifestream " equivalent for "we're all gonna die one day" thus only the dead can enter the realms of the lifestream?

Minerva shows herself to Genesis in a vision in the Lifestream. Looking into his soul and seeing his unselfish desire and will to "complete his duty as a SOLDIER" she "revives" him as a reflection of the Lifestream's will  -Crisis Core Wikia

( the next scene with Genesis is in a coma like state next to that chair) completing the last missing chapter of Loveless, after getting kidnapped/taken by those mysterious men (Nero and Weiss ) was that a reference to the next event presented later in Dirge of Cerberus? (in story time line of course ) as a "silent sacrifice" because that last chapter in loveless was also used in a reference to Zack's death and sacrifice taking on the Shinra army all by himself.