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Johto Sidequests

In order to do this quest you must have beaten the Johto Elite Four. Level 60-70+ Pokémon are recommended.
Note: You will not be able to leave the quest area until it is completed so be sure you are fully prepared before starting.

Starting the Quest

1a) To begin the quest, head over to the Pokémon Center at Route 32, then proceed down and to the right into the checkpoint gate.

1b) Continue through the checkpoint gate into the Johto Shipyard. From there, enter the far right building. Once inside, go through the side door and speak to Cpt. Jeck Spearow.

1c) After some dialogue you will go back outside and speak to Quartermaster Gibbs to start your adventure.

Finding Medic Mary

2a) Once you are on board the first task will be to find Medic Mary. To start, enter the door on the Main Deck.

2b) Continue further down into the ship by going down two sets of stairs, putting you at Ship Deck 1.

2c) Once you reach Ship Deck 1, walk north to the end of the hall and enter the door on the left. Inside you will need to speak to Deckhand Paul.

2d) Deckhand Paul tells us that Medic Mary is on the Main Deck, so we must head back up to speak to her.

Rat on Board

3a) Medic Mary tells you to report to First Mate Mike, who is located in Ship Deck 2. Proceed down into the ship once again, and you will find him in the top right room.

3b) When speaking to First Mate Mike, he will claim that there is a rat on board and that he needs evidence from the Crew Quarters. The evidence is found within the rooms on Ship Deck 1 and 2. During your search for evidence you will meet Shifty Pete. When speaking to him, use the following answers to collect evidence in his room:
“Who are you?”
“Sorry, I should not have asked”

After collecting all of the evidence, return to First Mate Mike.

3c) Next, you will need to enter the Ships Cargo Hold to speak with Cook Kingsly and Shifty Pete.

3d) After speaking to them, return to the Main Deck and climb the ladder up to the crow’s nest. Speak to Crowsnest Kev at the top.

3e) Now you’ll need to speak with Master Duncan in the Ship Galley. After speaking to him, return to the Main Deck and speak to Quartermaster Gibbs.

The Cunning Sly Rat

4a) Return to the Ships Cargo Hold. Once down there, run around until you get some wild encounters. Defeat a few Rattata until one appears on top of a cargo crate.

4b) Now that the Rattata is on the crate, you must interact with it from a specific direction multiple times to move it into a corner. If you interact with it from the wrong side, it will return to the starting position. The image solution is below.

4c) Once it is cornered you will have to defeat it in battle. Defeating it will drop the key which you must now bring back to Quartermaster Gibbs on the Main Deck. After that, return to Ship Deck 1 and enter the first door on the left. Interact with the cupboard inside the room and then enter the secret passage.

4d) Proceed through the secret passage until you find a room with Shifty Pete. Take the book from the desk in that room and proceed down the ladder. After finding out that the exit is blocked, return to Shifty Pete to find that he has found another way out.

4e) Upon exiting the room, report back to First Mate Mike in Ship Deck 2.

The Final Confrontation

5a) First Mate Mike will send you to the Captains Quarters to speak with Cpt. Jeck Spearow. The room is located at the very north end of the Ships Cargo Hold. During the dialogue with the captain, select these options:
“I found Smee’s missing diary”
“Yes, and he seemed scared of you.”

5b) Once Cpt. Jeck Spearow leaves the room, head to the desk at the back and read the “Note to Captain”. Report back to First Mate Mike’s room, then to the Main Deck. After that, speak to Boatswain Dave.

5c) After Smee walks the plank, report to First Mate Mike once more. He heads off to the Captains Quarters where you will follow. Cpt. Jeck Spearow will be waiting to battle you inside.

5d) Once the captain has been defeated, speak to Quartermaster Gibbs on the Main Deck. Go up to the crow’s nest once more to speak to Crowsnest Kev, who will say that we have landed somewhere. Exit the boat and enter the house on Mystery Island to talk to Smee.

That’s the end of the quest! You can now return to Johto by speaking to Quartermaster Gibbs, or explore Mystery Island to your heart’s content. There are a few daily battles here, including a boss battle vs Cpt. Jeck Spearow.

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