In this game, Dusknoir plays a good guy in the beginning, when you first meet him. Everybody thinks he is a great and famous explorer. He saves you a few times too. But when you capture the "evil" Grovyle (who's really your partner when you were a human), Dusknoir grabs you and your partner and drags you into another world. You end up battling him and several Sableye before going to Temporal Tower.
Despite its legend, Dusknoir is not a legendary Pokémon.
In the Japanese version, the Dusknoir Pokédex entry says it takes spirits to the Underworld. This could possibly be referring to Hell, a place in some religions in which the souls of sinners are taken in order to punish their sins. It was changed to the spirit world possibly because of the entry's morbidness and reference to religion.