If you're talking about ep 322, then it was David-Evil-Genius-Kemper. He said he originally wrote a different eppy that ended up getting so long, he had to turn it into a two-parter and slate it for later in the show's run (probably season 4) and write a whole new eppy for the end of season 3.
Personally, I would have been happier with ITLD2 as the season finale after another eppy between Fractures and IYYY. I just needed more explanations after Fractures... official ones, not those that I get from fan fic.
Love your reasons for chosing those fav characters. I, too, loved that Zhaan is a plant, and that they dropped hint throughout season one for that revelation. It's not the first time that I've seen a plant as a main character, but that was in a book, not a TV show, AND it was a LONG time ago, so it was a great reminder of some bitchin sci-fi details.
I also loved the helium-farts... and that was Rockne's idea.
And who can't love John and Aeryn?
Are you a shipper?