Some changes were made to Otacon's lab concerning objects lying around. Originally the anime poster on the wall was of Hideo Kojima's earlier game "Policenauts", which is changed in subsequent versions to a poster of "Zone of the Enders 2" and the Playstation lying on a desk is changed to a Gamecube with a Wavebird controller.

Two statues of Mario and Yoshi were also added. Shooting the Mario trophy plays the original 1-UP sound from the NES classic and restores a bit of Snake's health, while shooting Yoshi just makes Yoshi do his famous "Yoshi!" squeak.