The Time Capsule does not appear in HeartGold and SoulSilver. Why? Because, in that timeline, rather than placing restrictions, Bill scrapped the project after discovering that Johto-native Pokémon were incompatible. And what went so horribly wrong?
Johto Pokémon would go in, and something else would come out.
In place of the Pokémon sent through, an extradimensional Pokémon would appear, displaying the power to warp reality itself through its mere presence. Because these Pokémon were discovered through a glitch in the Time Capsule, they are sometimes informally referred to as "glitch Pokémon". (This, of course, is inspired by the Johto guard glitch in the original Gold, Silver and Crystal.)
When caught specimens escape into the wild, scientists become frantic in their attempts to recapture their missing number. (c wut i did thar)
In one story I wrote, one of these Pokémon, designated Specimen 000, was given Ex-serum, subjected to Delta irradiation, Shadowfied, and finally locked in permanent Burst mode with a human host. Introducing itself as "Novorien Malanimo", it was appointed High Commander of an evil syndicate's militia, gaining the nickname "Commander M." (a dual reference to Missingno. and its distant cousin 'M).
Commander M. has a plethora of unusual powers, chief among which is its Ability "Type Roulette", which causes it to randomly change its type combination every five turns. (This is inspired by the idea that, if Delta Species Pokémon existed in the video games, each Pokémon would likely have a predetermined Delta type combination, but Missingno., being a glitch, would have no Delta data, causing it to change at random.) Its signature attack, Stellar Impact, is essentially Sky Attack up to eleven.
So yeah, there's more or less how I would do it.
