According to a 1998 The Playstation magazine interview with the game's director Hideki Kamiya & writer Noboru Sugimura, they originally had no intention of bringing back the Tyrant, since the first game already had him as the final boss.

Kamiya thought of making him a "perfect, invincible Tyrant", but after the two talked it over, they realized it was a bad idea because he would be so strong that the G-virus would be rendered meaningless, so they came up with the idea of the Tyrant's mission to retrieve the G-virus instead.

Sugimura also commented on about the Scenario choice for the Tyrant:

"One of the consequences of having players go through the same scenario twice was that, by the second time, they’re used to things and it’s too easy. For that reason we decided to have the Tyrant appear in Scenario B, as a way to raise the difficulty."