James Vega, capitaine de l'Alliance Marine, doit former un groupe d'élite spéciale pour affronter un mystérieux extraterrestre, connu sous le nom de "The Collectors".

Ten years after the starship Voyager's return from the Delta Quadrant, the Federation is in a crisis. The Federation's main suppliers of dilithium crystals (the primary catalyst for the fuel used in faster-than-light travel) are disappearing. Space and time have folded around several planets, isolating them from outside contact. The phenomenon is unnatural – someone or something is causing it to happen. The need to stop this necessitates drastic measures, some of which are outside the Federation’s normal jurisdiction.

Trois enfants sont transportés dans le Monde numérique où ils doivent sauvegarder leurs zones spécifiques avec l’aide de Shoutmon, un digimon énergique habitant le monde.