Which for example? It's all performed well of course, but I don't really heard a memorable part.
A lot of this song stands out to me, but I'll do my best to pick my favorite parts.
I truly love the entire overture. It's gotten blasted by some fans for not being a "true" overture in the sense that it contains themes heard later in the work, but to me, part of being a progressive band is doing whatever you please and not confirming to rules. A lot of this may sound like a collection of Disney-esque themes played with crunchy guitars, but to me it sounds amazing.
Obviously, the second part of the song (especially when Russell is singing) is a highlight. The lyrics are beyond cheesy, but considering the subject matter it's difficult for them not to be. Romeo's clean guitar playing is pristine.
The section at 8:14 is another high point for me. There is something very ominous and Dio-ish about this section that I love. The keyboard, the groove... all of it.
9:12 is another great moment, since to me it sounds like a ship rocking back and forth through turbulent waves. This is especially true when the guitar starts playing those "funk" chords and the bass holds down that sick 9/8 + 10/8 groove.
The proggy section from 11:31 to 12:07 is one of my favorites of the song, although I'm the only person I know who would call it "catchy." It shows the entire band working as a unit to deliver one hell of an orchestral moment.
I like Circe - particularly the "calm before the storm" verse and chunkier ones that follow. Neat vocal harmonies, too.
The Sirens section is cool, especially the syncopated 7/8 sections after the verses. I love how the band changes the entire power of the riff by changing from a triplet feel to a straight feel.
The instrumental section beginning at 16:43 is awesome and demented. The apparent randomness (it's not) at 17:29 is another big moment for me. Considering this section is supposed to be about sea monsters, it works.
Finally, the entire mellow section beginning around 19:09 and leading up to Champion of Ithaca is amazing. And of course, the grandiose power metal epicness of the big chorus at the end is made so much more powerful due to the 20-minute journey that preceded it. I
love the crystalized delay effect used on the guitar during the final verses, too.