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Question: In your game, considering that Scions can beef up to God, can low level gods that have been around for a thousand years at Legend 9-11 use the times to revitalize themselves and reach Legend 12?

Yes, they certainly can, but they shouldn't unless that is in some way a useful or good thing for the PCs' story. Lower-Legend gods, while cool to interact with as NPCs, are not the stars of the show; the Scions are, so unless a Scion is involved in a lower-Legend god's ascension, they probably shouldn't be having one. You don't get Legend just for hanging around, after all; the Titan war is a great staging ground for the kind of awe-inspiring, insanely cool feats that cause a god to gain Legend, but the more of them you have being performed by NPCs, the fewer are available for the PCs themselves.

There are buckets of reasons Scions might be involved in that kind of a story, though; maybe they want to help a lower-Legend god make a name for themselves/get out of a rut/make a bid for political power. Maybe they become best friends with that god and call him in when shit is going down, leading to him being involved in a lot of the kinds of high-powered shenanigans that can cause Legend to increase. Maybe they marry lower-Legend gods and the force of their own fame and exploits helps carry them along. Maybe a lower-Legend god's attempt to rise to power is something that threatens the PCs or something they care about, leading them to oppose it.

But whatever it is, it has to be something that is about the Scions, not the lower-Legend gods. Otherwise, not only is it harder for your PCs to be cool (and trust me, if NPCs keep grabbing all the glory, PCs are going to get disgruntled pretty quickly), but they end up with the same problem of no gods their own Legend to interact with as they go up the ranks. If everybody is Legend 12 except the Scions, they have no one of an equal level to challenge them or become allies; they're still second-class citizens despite the supposedly important ascension to godhood at Legend 9. Gods at Legend 9-11 are very important to make compelling stories for PCs at that level, so if the plot doesn't have a very good reason that they increase in Legend, they probably shouldn't.

Also keep in mind that all the ancient strictures that make it hard for gods to gain Legend are still in place. Fatebonds are still a terribly scary force in the World; they didn't go away when the Titans broke out, and the whole point of having Scions is so that gods (of any Legend rating) don't have to go down there and get whammied with all kinds of mortal expectations. The political structures of many pantheons may have shifted some in wartime, but most of them are basically the same, and it's not as if laws and customs have gone out the window. Low-Legend gods of the ancient pantheons certainly could gain Legend, but if they haven't done so in thousands of years, chances are they're not about to start now unless something (i.e., the actions of the PCs!) helps or forces them.

So yes, absolutely; any god can always increase in Legend if he's not yet Legend 12. But make sure you have a good reason for him to do so; if it serves the story, awesome, but if it's just because you want a bunch of gods to be Legend 12 and don't have a particularly good reason for that desire, it's better to rethink and scale back.