"Spiral Nemesis" is the main conflict in the show. "Spiral Nemesis" is an event. Not an omnipotent being. It's a giant black hole that sucks in everything because spiral power grows out of control (Think http://en.wikipedia.org/wiki/Heat_death_of_the_universe
Every villain in the show as reacting to this. The Anti-Spirals wanted to stop Spiral Nemesis from happening, so they decided to seal the spirals away and keep them down. Genome couldn't win, so he stayed on earth and made sure no one came above ground, so the Anti-Spirals wouldn't attack, so Spiral Nemesis wouldn't happen. The village chief in episode 1 protected tradition to keep the people safe, from the Ganmen that Genome sent to make sure no one came above ground, so the Anti-Spirals wouldn't attack, so Spiral Nemesis wouldn't happen.
How do people misunderstand a kids show so much? Pay attention.