I see my favorite part hasn't been mentioned yet, so I have to chime in. Actually, it's two parts, and they've been mentioned separately by two different people, but it's when they're together that you hear the magic.
First is the lead that begins at 11:07 and goes to 11:25, where it's repeated twice. On its own, it's really cool. But then at 28:31, it returns. Again its played twice, and then a third repetition begins. But surprise! On the third run the lead melody drops down and starts charting another course, this time with a less-structured and more "jam" feel to it.
From an instrumental standpoint, it totally makes the song for me, because on one hand the repetition helps tie the 40 minute song together, and on the other hand, the variation the second time through lets you know that things are changing and you're getting closer to the end. It's the "release" of the album for me, and I always go "ahhhh..." or maybe "yeah!" when it finally comes.
I just checked the lyrics around those sections, and now it makes the song even MORE complete (although this may just be random dumb luck?) At 11:25, the lead ends quickly and a new, uneasy section begins with the lyrics "And with death came disorder, who were they now to obey? / No leader, no followers. / No trust, no faith." Then at 29:13, when the lead ends with considerably more swagger, the lines are "A leader was chosen to unveil the hidden truth. / The brave ones were gathered, the strongest were sent to the queen. / Her reason to be must be known." Also I just noticed that there's a little trill on the last note of the first cycle of the second appearance of that lead that's not there in the first appearance. Another sign of renewed confidence?
Anyway, yeah, what a great song.