In the game's opening cutscene after Dr. Yoshiyama digitizes himself, several blocks of what seems to be gibberish appear on-screen before the computer corrupts. This gibberish is actually a secret message written in Japanese romaji and then coded through a cipher where all vowels are omitted from the text, except for when a word starts with a vowel. Decoding the message reveals what seems to be the last conversation Yoshiyama had with the C-Life woman featured in the cutscene, the mother of Pulseman, suggesting that he gave up his human life ("Do you realize what you've done? You'll never be human again now.") out of love for his creation and resulting in the conception of Pulseman. A cosmetic detail hinting at the nature of the undeciphered message being a conversation are differences in the speed at which each text box appears typed out on-screen (i.e. a slight slowdown during "I'm just a heartless program"). However, not only does this affair reveal the origin of the game's hero, it also has implications about the origin of the game's villain.

Dr. Yoshiyama's whereabouts during the events of Pulseman are never stated, but through information provided in the game's manual, it is suggested that he was corrupted during his time in cyberspace and transformed into the game's antagonist Dr. Waruyama. This theory is supported by the manual listing Yoshiyama's entry into cyberspace during the cutscene and Waruyama's birthdate, December 31, 1999, as occurring in the same year. However, Waruyama appears to be a full-grown adult by 2015 when the main events of the game take place despite technically being 16 years old and less than two years older than Pulseman.

This age discrepancy suggests that Waruyama would have to be at least a half C-Life or full C-Life himself in order for him to originally have been "born" as an adult (given that C-Lifes are computer-generated life-forms), and in this case, for him to originally have been the adult Yoshiyama. Since Yoshiyama was implied to have transformed into at least a half C-Life following the deciphered conversation, this suggests that Waruyama's "birthdate" actually refers to the exact date when Yoshiyama was transformed into Waruyama in the first place.

Additionally, there are similarities between the two names, with "Waruyama" being similar to "Bad mountain" ("悪い山" or "Warui yama"), and "Yoshiyama" appearing similar to "Pleasant mountain" ("楽しい山" or "Tanoshī yama").

The English description for the game's 2009 re-release on the Wii Virtual Console states outright that Yoshiyama did transform into Waruyama, although there are no known Japanese sources that also confirm this.