Chicago represents Texas, their home, taken over by bad, bland pop music, as is the symbolism of the mutants. Aria is met here, after taking unknown trips, perhaps symbolizing Omar's hitchhiking expedition across America. Ogale is the variety of drummers they went through, none holding a candle to Jon Theodore or Thomas Pridgen. The car crash into the hospital represents various drug-influenced misadventures had by Cedric and Omar. Inside is Grave, or in the allegorical sense, Jeremy Ward. He was one of the most powerful influences on The Mars Volta, being their primary sound technician. Thus, he is shown as the strongest one. Verse, shown out of the canon timeline, is Thomas Pridgen - goofy, fun and cheery, but reliable to get the job done. The mall is representative of their journey creating the album De-Loused the Comatorium, and the monster is a metaphor for Julio Venegas, an old force from the past pressuring them in the present.
Marid is representative of Jon Theodore, someone Cedric and Omar were first infatuated with but then lost without much regret. The boat ride is symbolic of making the album Frances the Mute, as it happened shortly after Grave/Jeremy Ward's death.
More to come.