I'm not sure I understand the story
god of time has a legendary crashout when he discovers God exists. Which means he must have no free will I guess?
wages war on God with his Titan army and gets his ass beat. leaves behind an egg with his powers as part of his plans
fucks with things so that his titan army is thought of as a bunch of bastards to manufacture a faction war and people also remember him as a hero and the egg as his heroic reincarnation
war spills out into the human world and wrecks things. Aegiomon hatches meets Inori, loses her, and then goes back in time innumerable times to try and save her, splitting himself across timelines in the process
God takes one of those splits, wraps an anime character around it and sends it in to try and fix things
you do and kill Chronomon, which is exactly what he wanted, leaving Aegiomon to be his replacement.
this was all just a really elaborate suicide attempt because Chronomon didn't want to work for God or couldn't stand being a part of some cosmic hierarchy?