The episodes "CORNERFOLK", "CORNERGIRL", and "MISTERMANTICORE" weren't originally included in the series while their respective seasons were airing, only being added after season 3 finished airing. It has been said by the creator, Alex Casanas, that these, along with the Modern Day episode "THE TRINITY DESK PROJECT" and the episode "THE HOUSE IN THE OCEAN" from the spin-off series THE NIXONVERSE, are considered "reconciliations" of past series.
The episode "THE TRINITY DESK PROJECT" is made up of majority segments originally from a series by the same name. The original run of the series aired shortly before and shortly after the end of season 2, being unrelated to THE MONUMENT MYTHOS. The series was cancelled and replaced by a new series called THE AMERICAN ANATOMY. The two series were then merged into one, with the new series taking the original The Trinity Desk Project name, and THE AMERICAN ANATOMY's episodes being added to the latter half of the series. The new version of the series was cancelled and pulled due to Alex Casanas, the creator of THE MONUMENT MYTHOS, The Trinity Desk Project, and THE AMERICAN ANATOMY, feeling as though the series was too similar to THE MONUMENT MYTHOS to warrant its own existence.
Every season has had some of its episodes aired out of order. This is due to each episode airing not during a regular cycle like most shows, instead being released upon completion. This has lead to the restructuring of some of the series, with one of the most notable examples being that LINCOLNLOOKER, the seventh episode of season 1, was aired as the third episode.