To me Illumination Theory works as a whole thing. There are even recurring themes to bind it together.
Set up themes
Life is painful
Life can be okay
The truth is painful
But if you embrace that pain, you will see the light
The music and lyrics both tell a story.
I commented on this in the Illumination Theory appreciation thread, so I will just transfer here a modified version of what I said since we are talking about disjointedness. IT is very cohesive for me because of the symmetry of the song.
Section 1: Paradox of the Black Light. Slow, majestic, a bit heavy so it is not yet "illuminated". This is an overture to the un-illuminated sections of the song.
Section 2: The heavy riffing section. At first this seems to be just a wanky instrumental but it actually acts as a bridge between Section 1 and Section 3. This serves an important narrative function once we get to the later sections. Note also that it is mostly a standard rocking beat, with some time signature changes only at the end upon approaching the Live, Die, Kill section.
Section 3: Live, Die Kill. The section poses the questions: What are you willing to live for? to die for? to kill for? It is asking for "an answer that begs to be found". The section has two subsections: the first has lyrics playing to a main riff, the second is the instrumental section that has plenty of time signature changes.
Section 4: Embracing Circle, ambient section. If Live, Die, Kill referred to a more down-to-earth plane of existence, to grounded reality, the Embracing Circle is situated in a transcendental plane. The ambient section is formless and lengthy, which signifies that the questions posed in Live, Die, Kill remain unanswered even in a moment of transcendence and it remains quite unanswered for a long time. The length of the section is important because it serves the narrative function of indicating that illumination or enlightenment does not come easily.
BREAK in the Narrative: Now we start to mirror the previous sections.
Section 5: Embracing Circle, orchestral section. This mirrors Section 4. We are still in the transcendental plane, but unlike Section 4, illumination starts to creep in slowly with the build up of the orchestral part. Illumination climaxes with a moment of enlightenment, signified by the orchestral version of the intro melody. It sort of mirrors Section 1 as well. The end of the orchestral section is an overture to the "illuminated" section of the song, The Pursuit of Truth. It will not serve its proper narrative function if it is placed at the start, because the more heavy-sounding music of Paradox of the Black Light better fits as an introduction to the "un-illuminated" Live, Die and Kill section. The two overtures share the same melody.
Section 6. The Pursuit of Truth. This mirrors Section 3. The section starts with reverse swells, which signals a return from the transcendental plane to grounded reality. After the moment of enlightenment in The Embracing Circle, the song now has answers to the questions posed in Live, Die, Kill. What are mothers willing to live, die and kill for? Their children. Husbands are willing to live, die and kill for their wives. Martyrs are willing to live die and kill for the kingdom. And so on and so forth. The Pursuit of Truth answers the questions of Live, Die, Kill. Still mirroring Section 3, the section also has two subsections: the first has lyrics playing to a main riff, the second is the instrumental section that has plenty of time signature changes.
Section 7: The heavy riffing section. This mirrors Section 2. It follows the same structure and uses the same riff! This serves as a bridge between Section 6 and Section 8. While Section 2 bridged the Paradox to the questions, Section 7 bridged the answers to the Paradox. Like Section 2, this section has a lot of wanky instrumentals and plays to a standard rocking beat, with a change in the tempo at the end approaching the Surrender, Trust and Passion section.
Section 8. Surrender, Trust and Passion. And now we have come full circle. This mirrors Section 1. Section 8 is also slow and majestic, but unlike Section 1, it is uplifting because illumination has already been achieved. Section 1 is titled the Paradox of the Black Light, and the lyrics in Section 8 spell out the paradox. And if I overanalyze the lyrics, even the lyrics here are symmetrical. LOL
Introduce with a paradox:
"To really feel the joy in life
You must suffer through the pain"
Surrender: Lyrics refer to illumination by referencing light.
"When you surrender to the light
You can face the darkest days"
Trust: Middle section, still in keeping the visuality of the Illumination Theory, we refer to opening one's eyes.
"If you open up your eyes
And you put your trust in love
On those cold and endless nights
You will never be alone"
Passion: Mirror the Surrender subsection. Lyrics refer to illumination by referencing bright.
"Passion glows within your heart
Like a furnace burning bright"
Mirror the intro. End with a paradox:
"Until you struggle through the dark
You'll never know that you're alive"
And as one more bit of analysis, which may be stretching a bit. Paradox of the Black Light started with a crescendo drum roll. Surrender, Trust and Passion ends with a decrescendo drum roll.
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This is how I viewed IT. Which is why I don't think I will really understand how it can be described as disjointed. It is very cohesive not just lyrically but structurally as well. The disjoint that some people feel, I think, is because the narrative of the song is really about transitioning from dark to light but ending up in a paradox where light is in the darkness. There is a deliberate disjointedness, from grounded to transcendent, from fast to slow parts. The transitions serve a narrative function.