The group has stated they intend to make a three-part story. Two of the parts are complete. The third is currently in outline form: "All out war." according to Commander. The overall story as envisioned by the group is tragic, and Panther says he "doesn't really expect it to end well for humanity."
Act I (The Protomen) - September 3, 2005

In Act I, the band's first album, Dr. Wily is represented as an Orwellian ruler over a dystopic City, full of humans who are too scared to stand up to his control. Dr. Light creates a "perfect man, an unbeatable machine", Protoman, to fight to free the City, but Protoman is destroyed by the overwhelming power of Wily's armies. Defeated and despairing, Dr. Light then creates a second son, Megaman, who he attempts to dissuade from battle. Megaman runs away from home and confronts his brother in an apocalyptic concluding battle.
The album has been described by the band as "the sound of the end of the world" and straddles the line between chiptune and hard rock, with heavier focus on distorted 8-bit synthesizers and electronic instrumentation.
Commander has stated that Act I "was made specifically to go against everything our recording teachers and fellow students were trying to feed us about making everything sound pristine and perfect". "Due Vendetta", the first recorded track, was actually completed in April 2003. (see The History of Due Vendetta) The album was recorded over two years in various MTSU and home studios in Murfreesboro, using analog rather than digital production techniques. The album was produced by former member Heath Who Hath No Name. The cover art and packaging for Act I were designed by band members.

Father of Death (limited vinyl 7" single) - November 8, 2008
Produced by Alan Shacklock, with Robert Tepper's "No Easy Way Out" as the B-side. Limited print run in white vinyl, a special advance of Act II. Unlike most of the group's output, was not released through the SoundMachine label. Instead, it came out through Theory 8 Records. Art design for the cover was produced by Version Industries. The release party was held at 12th and Porter in Nashville. The version of Father of Death presented on this vinyl varies significantly from the Act II version - slower tempo, deeper/more seperated acoustic guitar lines, and an overall brightness and clarity that some feel was lacking in the final release.
Act II (Act II - The Father of Death) - September 8, 2009

For the band's second album the group, working with Meatloaf producer Alan Shacklock, devised a prequel storyline to Act I. The second act details the rise of Albert Wily to power, the rivalry between himself and Thomas Light, and the tragic events which brought the City under Wily's control. The band states that Act II was designed to sound cleaner, reflecting a time "before the bomb dropped".
Accordingly, the second album reflects a much broader range of musical styles and more lyrical instrumentation, embracing references from Ennio Morricone to Bruce Springsteen to Shacklock's own Babe Ruth. The album was mastered by Richard Dodd, a Grammy-winning recording engineer, and as before, recorded in several locations. The cover art, a deliberate callback to the art for the 80's movie Streets of Fire, was executed by artist John DeLucca. The Act 2 logo was designed by Version Industries. An incredibly massive release party was held in Nashville at Mercy Lounge on Sept 25, 2009.
Act I (Limited Release Vinyl Remaster) - July 9, 2011

A short-run 977-piece remaster of Act 1 on special bi-colored 12" vinyl was released on July 9, 2011. A special performance (recorded for eventual DVD release) was held at 12th and Porter in Nashville to celebrate the release. The vinyl came with a special white stencil and a large fold-out version of the libretto with new artwork. In addition to the extra goodies the tracks were fully remastered and the original ending, "Fade to Phil", was included, a disturbing track of sheer noise overlaying a broken 8-bit refrain from Phil Collins' "Against All Odds". Numerous small changes were made to the original tracks to increase their depth and richness. New sound effects were inserted at the end of Hope Rides Alone.
Later editions of the vinyl, the band states, will be normal black plastic.
Miscellaneous notes
All albums release through Sound Machine Records, the group's private label. The CD booklets contain vital story details as well as full lyrics, and are an important part of how the band desires their work to be experienced; therefore, people are highly encouraged to buy physical CDs rather than digital copies in order to have the full experience of The Protomen's story.
The Protomen have expressed interest on several occasions in creating soundtracks and film scores.