u/Ultimatonium

I've started watching Bones out of curiosity and got hooked on the Gormogon plotline. Which suddenly endet after Zack confessed.

Now after I've watched all all 12 Seasaons I'm extremly confused. What happend to the Gormogon plotline? Why did Zack confess? Wasn't the Master that old guy in the retirement home? Later Zack withdraw his confession because of.. why?

For me it seems they suddenly abandoned the whole plotline and made a quick hotfix at the end to redeem Zack.

Can anyone explane what I've missed?