First thought: the rebels are slightly hypocritical. They condemned Nine for abandoning them in season one, but then when some innocents were stranded in a dying world they were both willing to abandon them and didn't help in the rescue mission because bigger picture.

Then during the final battle, the rebel version of Knux entrusted an entire unit to a man that he had seen refuse to save his own crew from death because there was nothing in it for him.

Meanwhile, Nine did abandon them originally with the Chaos Council's power shard, because he trusts basically no one, but the rebels don't know that and they did hear the Council coming looking for Nine right before he bailed. And he came back later and helped them in the next main fight...

...at which point he was captured and made to help in the events that led to the literal decay of their universe.

After his fallout with Sonic and subsequent bullying to make Sonic surrender to him (admittedly villain-ish actions), he agrees to fix everyone's home as part of Sonic's terms

And literally the whole multiverse goes "Nah, we know you loudly announced that you just wanna fix your home for the world to hear, and that you're the only one who can fix the problem and save us...but we know what will REALLY happen if you get what you want so we're renagging on the deal to force you into submission instead".

Which is proven to always work.

And given the word of God is the universe just ends anyway, I'm just here going "So the correct answer was for Nine to take the shard, fuck off to another world, never return, and seasons 2 and 3 would never have happened therefore the universe would still exist. Also the rebels would have won their war eventually after the Council's backup power ran out."

Because that's what I'm getting. Nine should've been a selfish asshole.

End of thoughts.