These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Alternative Character Interpretation: Some fans of OM1 prefer to think that both Dr. X and the anti-government conspiracy only exist in Nikki's paranoid mind. In this view, Mary was either a complete fabrication, or an innocent nun whom Nikki fixated upon, and eventually murdered in his delusional state.
Crowning Music of Awesome: The original Mindcrime has been lauded as one of the best heavy metal albums of all time. It is also considered one of the first examples of progressive metal.
And in specific to the album, the last track concludes with an increasingly louder and more congested cacophony of music, sounds and voices from the rest of the album, which — if you have allowed yourself to fall into the world the album creates — very effectively feels like what the inside of Nikki's head must sound. Then, as it reaches a crescendo, it rings to a sudden, complete, spine-tingling silence with just Nikki's voice saying, "I remember now"
Fanon Dis Continuity: Many fans weren't too pleased with the storyline of OM2, especially the second half, and consider only the original album as canon. (Imagine the vindication they felt when Michael Wilton admitted that the second album suffered from Geoff Tate doing an I Am the Band.)