An alternate DNA Soul item with four sections. Basic enemies only drop the 1-3 segment variants – worth 4, 8, and 16 DNA Souls, respectively – and the bosses only ever drop the 5 segment variant – worth a whopping 200 DNA Souls! While not technically unused, the only one in the game is dropped by Sigma after the final battle. It's worth a decent 100 DNA Souls, but since the player can't save the game after that fight, it can't be used.
A small Weapon Energy capsule, taken straight from the previous title. Unlike that game, enemies do not drop regular Weapon Energy, only the DNA Soul counterparts, and the only regular weapon energy, placed in any stage in this game, is a single large one in Launch Octopus' stage.
The most noticeable difference here are the color changes: Japan got a light green color, while the international versions were stuck with purple. The "Press Start" text was also moved lower in the international versions to accommodate the larger title.
In the Japanese version, Flame Mammoth's stage plays the music used for Launch Octopus' stage in Mega Man X and vice-versa, which was corrected in the International releases.
Another glitch exclusive to the Japanese version allows you to reach the credits early; during the final stage the EXIT option in the pause menu is disabled, but due to an oversight it can be used during the boss rematches which causes the game to jump to the ending sequence.
There are three notable typos in this game that went uncorrected in the Virtual Console re-release.
The Reploid Research Laboratory is mistakenly referred to as the "Reploid Research Lavatory" during the introduction sequence.
During the cutscene in which X and Zero encounter Sigma, the latter says, "Now is not the time to talk, now is the time to destroyed!" He also includes an unnecessary comma in "You know, that I'm going to destroy you."
During the ending, X says that the "DNA Soul are returning".
Some parts in the Parts Shop have an unlock requirement that's impossible to avoid in normal gameplay. This is because the Intro Stage boss, Skullhead, always gives the player 200 DNA Souls after being defeated. The unavoidable parts are as follows:
