Its an awesome track, i enjoyed it; but technically nothing unusual happens until the Avant-garde bit at the end.
The general idea seems to be a variation around a C# minor theme (from the 9th fret on the g'tar);
Bass: is playing F# B C# then an open E string run E/F# E/Ab B/C (I think :))
Guitar: is alternate picking Ab its 5th(Eb) / Ab its 4th(C#) / Ab its flat 7(F#)
The rest is a variation on this at different velocity, if you figure out the first bit you'll have the rest no probs.
The picked notes by the guitar almost make up an Abmin7 chord, which I think i heard strummed as a chord in the quieter interludes and towards the end of the song.
And actually, the bass provides the B(flat 3rd), which is the missing tone from the guitar picking section.
Its ok to play C# Dorian over this Abmin7, since it shares the all the same notes as Ab minor; and all the notes of Abmin7 (Ab Eb F# B) appear in both Ab minor(C# Dorian) and C# Minor. (And in fact I think the last section; before the drum bit ends up in Ab minor)
Thats the only thing going on in this really; and its brilliant; its the kind of thing i like to do a lot.