It starts with the [[S.S. Libra]] cruising, when suddenly some helicopters appear with [[Shadow Lugia]], which picks up the ship as the sailors that fell out watch in awe. Then, [[Michael]] finds himself using [[a {{p|Salamence]]}} to battle [[a {{p|Metagross]]}}. No matter what the outcome is, the player will then find himself in the [[Pokémon HQ Lab]], where the trainer will tell him to consider raising Pokémon other than [[{{p|Eevee]]}}. Michael then speaks with [[Professor Krane]] and [[Lily (XD)|Lily]]. Prof. Krane comments Michael's skills, with Lily worrying that Michael will become spoiled. Prof. Krane tells her not to worry, saying both Michael and his sister [[Jovi]] are both wonderful kids, reminding Lily that she hasn't seen Jovi since lunch.

Lily asks Michael to look for her. Michael looks around, finding a [[P★DA]] that Professor Krane left him in his room and gets an E-mail telling him to ask [[Adon]], who was playing hide-and-seek with her. Adon tells him to look at [[Dr. Kaminko]]'s house. Michael then sees a report about the missing cargo ship that was carrying loads of Pokémon, the S.S. Libra. Michael goes to Kaminko's house, where he is attacked by [[Chobin]], who mistakes him for a burglar and sends out his Pokémon. After fending him off, Jovi shows up and asks what Michael is doing and asks if he is lost. Jovi then acts all high and mighty saying she knows that he is lost. Michael goes inside, and Chobin shoes a video of himself bragging about Kaminko's inventions that are harmful to mankind. Michael tells Jovi that It's time to go home, so Jovi calls back her [[{{p|Minun]]}}, [[Mimi]], and follows Michael back to the lab. Jovi continues saying Michael was lost when Lily scolds her.

Jovi goes to find Aidan, as Michael talks to Prof. Krane and obtains the snag machine. Aidan adds a Shadow Monitor to the P★DA, and Professor Krane goes to ready the battle sim. However, some men come in and take Professor Krane away. Michael goes outside and finds everyone knocked out. Michael then battles the leader, [[Naps]], who is using a [[Shadow Pokémon|shadow]] [[{{p|Teddiursa]]}}, which Michael snags. Prof. Krane is then dragged away by the kid nappers, as Michael watches in despair. Jovi is crying, and everyone looks sad, Aidan says Prof. Krane is crucial to the Purification Chamber project, and that there is nothing they can do. Lily then says they can complete it themselves, though Aidan says it is hopeless. Lily says they are on the verge of finishing and walks off, and Michael follows, starting his journey.