Helix Season 2 Finale, Anyone? *SPOILERS*

Just got thru that finale of season 2 of Helix on Syfy. I gotta tell you, the season two was full of inconsistencies, annoying, several plot holes and a lot of stupidity.

I found the show on Netflix a few months ago and was impressed with season 1. That claustrophobic environment in that ice station on the North Pole. Season 2 we find them on a tropical island with some David Koresh type character ruling over his goofy followers. They kept jumping ahead 30 years (Why is beyond me, it was just confusing and a waste of time) .
Then there was the case of Amy...
Was she made immoral? They showed that her eyes had not changed and she was exposed to the gas the Coast Guard spayed on the island. It burns her skin and she falls down, presumably dead. We see her body being dragged off and in the next episode, Peter and his new "love" have gathered the bodies and start to chop them to pieces and Amy's body is the first they to to work on. At least it looked like her (?) I dunno.

In the finale we see her alive but very deformed. I thought : wait a minute. Did the writers forget about the previous episode? Huh..?
Alan told the other doctor about a safe deposit box with evidence but we see them arrest his brother Peter. I mean the feds were after Alan so why are they leading Peter away in cuffs.
Then in the final scene, they flash forward 15 years (what, not 30? ) and Dr. Jordan is running some bizarre fertility clinic. The first season finale jumps ahead one year and we see Julia has joined Ilaria. Now Jordan is running some....
Someone help me or put me out of my misery.