I would prefer the Ultimate Universe stay true to its deeper purpose of more realistic political and social themes and create a more plausible virus with longterm consequences, like any real virus. Perhaps they could contain an outbreak, but there shouldn't be a clear-cut cure that undermines the purpose of the virus altogether.
To make it interesting, perhaps it can be an STD like HIV and AIDS... This would protect the central cast, but for small groups of mutants living on the streets, the disease could become quite formidible. Hospitals would be afraid to treat them and they would be pushed out into the streets to die.
Perhaps this would be where the Ultimate Morlocks would come from... Dying homeless mutants forced to live in the sewers with little or no treatment. Perhaps storm would be infected somehow.
They could introduce mutant named "Patient Zero" mirroring Gaetan Dugas, the gay flight attendant whom they linked almost every case of AIDS to in dozens of major American and Canadian cities back in the mid-eighties. His sociopathic and reckless behavior destroyed countless lives.... It'd be interesting to see that sort of dangerous criminal in the Ultimate Universe.
It would also be interesting to see a much different Illyana Rasputin... sold into the sex trade only to discover she was a Mutant and that she contracted the Legacy Virus.
