The game starts out by letting you pick your name, which then leads to an animation of the luxurious cruiser Libra sailing on a smooth sea during twilight. The captain and the sailor in the control room suddenly spot helicopters surrounding their ship, and a giant shadow looms over them. One of the helicopter pilots flashes a red light from his eyeshield, and the eyes of the creature, which is Shadow Lugia, shines with the same light. The ship is then sucked up into the air by Shadow Lugia, and the captain and sailor are thrown into the waters. Floating amid the stormy seas, the two could do nothing but watch their cruiser get carried away by the creature and the gang of helicopters.

The Pokémon HQ Lab:
The plot begins in a virtual battle between your level 50 Salamence against a level 50 Metagross belonging to a virtual trainer caleld Maibo. Your Salamence has earthquake so it should take care of the Metagross pretty easily. Beat it and you will be transferred back into the real world.

You are greeted by a young trainer and researcher in charge of the virtual trainer machine, and you find youself in the training room at the Pokémon HQ Lab directed by Prof. Krane. You have your starter Eevee in your party which is at level 10, and in its description says it is given to you by your father, who has passed away.

You head to Prof. Krane’s room to the left, and he will tell you to retreive the P*DA at your own room. Your mother, Lily, says your sister, Jovi, is missing, and wants you to go in search of her. Enter the left door in this room to get to the connected building next doors. You will find yourself in the researcher Buster’s room. Go into the left bottom room of this floor to find a guy named Haido hiding under a table. He will tell you that he is playing hide and seek with Jovi, and tells you that she is probably at Prof. Kaminko’s house. This new location shows up on your map, and you can now access it.

But first, go down to the first floor to retrieve the P*DA from your room, which you should receive a welcome message from Krane right away. The only features on your P*DA right now will be the mailbox and strategy memo. You will see a Plusle in Jovi’s room which is right next to yours. Other overworld Pokémon in the lab include a Kecleon in Haido’s room, a Kirlia and its Elite female trainer, a Psyduck and Quagsire in the common room where several researchers are watching TV, and a Blissey on the first floor right next to the HP restore machine, and later the Purify Chamber. You can only read the OBNS news on TV, which talks about the Libra incident, and some researchers will comment that lots of rare Pokémon are riding on the cruiser, including ones that have never been seen before. You can now leave this place.

Prof. Kaminko’s House:
This eerie house to to the southeast of the Pokémon HQ Lab, and the first thing you see is a Groudon statue in the center of a fountain. Go to the house’s front door, and Kaminko’s assistant Chobin, will mistake you as a thief and fight you.

Researcher Chobin: Sunkern 5

Defeat him, and Jovi will come out from the house. She tells you that she is having fun, and goes back in. Follow her, and Chobin will brag about the ‘mighty’ inventions of Kaminko, including something known as the Shuckle Shoes. The door on the right is locked right now, but head in the left one to find Kaminko. He will not let you enter his secret room at this point. You receive another mail from Krane, and talk to Jovi. Calling back her Minun, she will then join you, and the two of you head back to the Pokémon HQ Lab.

The Pokémon HQ Lab:
Back at the lab, Prof. Krane will tell you that one of the researchers, Joshua, has successfully completed the Snag Machine after modifying it from the one made by Team Snagem 5 years ago. It is now equipped with the Aurora Searcher to detect shadow Pokémon, and you agree to test it out for them. The shadow Pokémon monitor feature is added to your P*DA, and Joshua will give you 5 Pokéaballs.

Suddenly, you will hear a cry, and head out to find Prof. Krane seized by three mysterious troopers dressed in white. You rush up to stop them, and one of them will fight you:

Mysterious Peon Spy Naps - Teddiursa 11+

Your Aurora Searcher will detect it right away, and Krane wants you to try a Pokéball. You will not be able to use attack commands at this point, so just throw the ball, and you should capture it without difficulty. Spy Naps will be outraged at you did, and together with his two mates, tossed Krane onto their truck and leave.

You will then find yourself back at Krane’s room, and everyone is upset. The researchers will worry about the Purify Chamber’s research progress which is headed by Krane, but your mom Lily will decided to take over herself since it is the project your father has devoted his entire life to anyway. She will want something some machine parts from the Gateon Port, and this new location will show up on your map. Together with Jovi, the two of you head there. But before that, Joshua will give you Krane’s Memo 1 and 2, describing what the Snag Machine and Aurora Searcher are about.