Season II is almost an "Alternate Universe" for MillenniuM, it steps outside of the original storyline set up in Season I, into areas of madness and spirituality that Season I merely hinted at in the four "Lucy Butler/Mabius/Judge/Al Pepper" episodes of S1.
Season II started and Ended with the Comet. As Season II Opened, it shows the comet entering the solar system near Earth. In that same Graphic in S2E1, we also see another, "unluckier" comet entering the Sun. As season II closes, this is referred to in Laura's "Vision". This aspect of "Luck and Chance" is also touched upon, it is a common Theme for Morgan/Wong.
Morgan and Wong were handed control of this show and asked by Fox to make specific changes and emphasis, some of these were asked for my the Fans, others Fox just wanted to happen. The Fans asked for a deeper look into The MillenniuM group, and we got this. The Fox Network wanted some tension between Frank and Katherine, and they got that- But for us it was never really resolved.
This episode capitalizes on Frank's true friendship with Laura Means and his apprehensive relationship with Peter Watts and The Group. In this episode, Peter is still Frank's friend, and I don't think that changed in Season III. What ultimately happens to Peter in this episode partially explains his strange behavior in Season III, until the final episode of the Series.
And the last we had seen of Laura, she had accepted full membership in The Group. But starting in "Owls/Roosters" we had seen Laura starting to break up - The first hint of this was when we see her smoking a cigarette. Peter partially addresses this when he tells Frank the reason why, and Patti Smith's song "Horses" gives us a visual in to Laura's Frame of Mind and explains the rest.
I can't compare this to the end of "2001" because the "Seven Minute Music Video" portion of this episode shows us some important imagery. The most important being her image of the Comet as a doorway, and there is still the other Comet falling into the sun.
In fact, if you consider that section as a music video, it is probably better than anything I have seen on MTV or VH1. If you pay attention to the images, it becomes much more than a Music video - It becomes a viable part of the storyline: and if we have watched the whole season including Darren Morgan's two "Humorous" episodes, pieces start falling into place. I don't consider Darren's two episodes as "Filler" - But as important aspects of Frank's Nature.
For me this caps off some fine work, some of Morgan/Wong's finest, there are several references to other shows they have worked on, "The X Files" (A Morley Cigarette Butt, but was it The X Files' "CSM" or was it Laura?) and "Space Above and Beyond" (Laura rolling multiple "Hard Eights") - "Choice or Chance?" which was a common Theme in "Space Above and Beyond"- And Also Kristin Kloke's breakout Role- A show which is proudly referred to in several of Season II Eps. But in one of Laura's final rants, she brings up the "Choice or Chance" aspect of her relationship with Frank- Did they choose their friendship, or was it determined to happen from the start of Creation?
And there are several things in here that make this probably the most painful Episode of MillenniuM for me to watch- Not just what happens at the end. For me this is rewarding TV Viewing, if you sit through it and try to understand why certain things are shown and said, if sets up the final 22 Season III episodes.
As far as issues brought up in Season II, these are deftly dealt with here- Frank's Father, Jordan's "Dreams", The Yellow House, and the scope and depth of The MillenniuM Group.
It is all brought to fantastic Closure, and when Chris took over in Season III, he had to build upon the framework set up here.
My Only complaint was that the ultimate Fate of Laura beyond what happens here is never looked into, but maybe that was the point of Frank's final scene with her.