The virus in the movieWas created, either through intent or unforeseen side-effect, by ZeedMillenniumon, during the events of Brave Tamer. Because, really, who else would want to do this? Even if Willis believes that he created it, no matter how good his programming skills are, it should have neither the power, the the compatibility or the sentience to have such disastrous effects on Chocomon/Lopmon/Wendigomon/Antylamon/Cherubimon, because he's A) human, and B) not the Monster Makers: There's no way he would understand, even somewhat, the digital monster source-code or programming language. Nothing that a helping hand from good ol' Mille wouldn't fix, eh?
- The Virus could have been Parrotmon reincarnated (just as Greymon from segment one was reincarnated as Tai's Agumon), that it fused with the Digi-Egg in segment two to become Diaboromon, and that the Virus in the last segment could have been what remained of Diaboromon after his defeat at the hands of Omnimon. This makes sense to me because it would present a Foil to the reincarnation of good digimon present throughout the movie (since Parrotmon was more predatory, and thus evil, he Came Back Wrong) and it would serve to connect the events of the film more.
The Willis/Cocomon-virus stuff never happenedbecause it was purely the result of everyone being high as satellites at the time. The theory that it was all them being on LSD would neatly explain everything; both the surreal surroundings and incidents, how they walked from New York to Colorado, how they flew from Japan to America, how the aforementioned two journeys happened within a day's time, and how four Rookies could turn over a Mega. As for Ken, he was wandering naked around Shinjuku. Cocomon's spiel is to advocate common-place drug use, ie, "'destroy' the social taboos on mind-altering substances". He meant to say the whole thing, but he was too stoned. Likewise, 'time to heal', rather than being a throw-away line, was advocacy of medicinal marihuana.
Hurricane Touchdown! took place between the Digimon Emperor arc and the Archnemon arc.They were celebrating the defeat of Ken (who was temporarily amnesiatic after his defeat; recovering in time to fight the Dark Spire Constructs) with Kari and TK visiting Mimi in New York, while Davis and the others had a beach party. Davis, having used the Golden Digimental of Miracles against Kimeramon, would be familiar with the operation of them, which meant he could inform Wallace how to activate the Golden Digimental of Destiny. Angewomon and Angemon evolving into Seraphimon and Holydramon, however, just kinda came out of nowhere, as did their new ability to summon the Golden Digimentals.