(Viper squadron is very confusing. The story is way too long to explain but if you have the time read the phantom RPGs and Assualt on sector 64. Jax basically changed time so a sith lord could not control the galaxy. He then came back to his own time and stopped the chain of events that led to the conclusion of the sith lord destroying evrything. But as we all know changing even the slightest thing has a consiquence. Jax then fought against Zion and won (woooo!) Jax then wanted to retire but decided not to when he realised he had created the riff and loads of people came though and made matters worse)
I know what you're thinking, I know how you're feeling, Believe me. You're not alone.