MGS2 & 3 were removed from digital stores.
The rats that appeared on Metal Gear Solid's Shadow Moses island ended up being a fairly unremarkable addition to the game, although there was a hidden codec call Snake would receive should he gun down too many of them. Director Hideo Kojima originally had other plans for the rodents though, none of which would go on to make it into the final version of the game. Said plans would've departed from MGS' stealth roots, while at the same time playing into the series' quirky sensibilities.
In an interview covered by YouTube channel Metal Gear Solid PS5 remake, Kojima may finally be able to fulfill his original plan of Snake raising his own furry friends.
Metal Gear Solid Could Have Been A Pet Sim
Metal Gear Solid 3 & 5 both went on to allow the player to tranquilize and capture rats, although there is still yet to be a Metal Gear title that allows the player to give them names. Given Konami's seeming lack of interest in the franchise following Metal Gear Survive, the prospect looks increasingly less likely. Kojima also had other idea's surrounding the rats, as he also originally planned for them to grow in size when shot but ultimately decided it was too silly and removed the Easter egg. It would seem that Kojima gave Shadow Moses Island a lot more thought than players might have realized, although that may not be too surprising given that Metal Gear Solid streamers discover new glitches to this day, proving that even a game as old as MGS still holds secrets to be discovered.
The Metal Gear Solid series is also known for including lighter moments within the often dark storylines, but it remains hard to see just how this mechanic would have been implemented in a way that made any real sense to the player or the narrative, given Snake's status as an elite soldier. The player, and by extension Snake, is also in frequent with numerous allies via the games codec system, as well as having allies within the facility itself, seemingly ruling out loneliness as a motive. Ultimately, it may have come down to the simple fact that Kojima liked the irony of a Snake raising rats in Metal Gear Solid.
Source: DidYouKnowGaming?