The film opens with a shot of the S.S. Libra cruising through the sea, when suddenly some helicopters appear overhead with Shadow Lugia, which picks up the ship. The sailors fall out and watch in awe as it flies away, carrying the ship with it. At Gateon Port, Jovi runs into Zook, who sends out his shadow Zangoose in anger. Before he can do anything else, however, a mysterious wealthy man, Mr. Verich, steps in and has one of his bodyguards defeat Zook. Michael and Jovi retrieve the machine part from the mechanic Perr (snagging a few Shadow Pokémon on the way) and return to the HQ lab.