Accomplishment of the quest's requirements
In order to move forward at the Manaphy quest, you need to be Hoenn Champion and be able to travel between regions. You also need to have 6 level 100 Pokémon, to not struggle against the questline's NPCs.
Eumi Island and the beginning of the quest
To start the quest, head over to the Lilycove City Port. Once you are there, interact with Sailor Jacob. He will ask you if you want to go to Eumi Island, press "Yes" and you will be teleported to Eumi Island Town. Once you reach Eumi Island Town, head north into Eumi Island Theme Park 1. When you will try to go deeper into the theme park, the receptionist will stop you saying they are experiencing blackouts and that Wattson reported some problems in New Mauville. From there, head back to the ports, sail back to Lilycove City and head to New Mauville, which can be reached by surfing south-east of Mauville City. Once you are in front of New Mauville, interact with the Officer Shamac and Wattson. After you've talked with both Officer Shamac and Wattson, head back to Lilycove City.
Black Ship and Captain Phantom
Once you are back in Lilycove City, head east until you arrive in front of a black ship and enter it. There will be 2 guards blocking it, but if you followed all the steps accordingly, they will disappear. Once you are on the ship, make your way to the top by defeating all the trainers you find on your path, taking note that their Pokémon are level 34 - 44. When you reach the Captain Phantoms Cabin, go up until you will find the Captain Phantom and defeat him. For a full list of the NPCs' teams, check the following page: Captain Phantoms Ship. Once you've defeated the Captain, he will give you back the machine part. From there, head back to New Mauville and interact with the Officer Shamac and Wattson. Now that you've returned the machine part to Wattson, the director of Eumi Island Theme Park will give you the complete access to the Theme Park Area. Head back to Eumi Island and then head north into Eumi Island Theme Park 1. The receptionist will now let you pass.
Eumi Island Theme Park 3 and how to catch Manaphy
Once you are in Eumi Island Theme Park 1, head to east until you will reach Eumi Island Theme Park 3. Once you're there, interact with the NPC Lyzabeth and she will show you Manaphy in its Egg Form. After that, Captain Phantom will appear, steal the Manaphy Egg and a member of his crew will battle you. His Pokémon's level range is around 60 and are: Arcanine - Dusknoir. Defeat the grunt, talk with Lyzabeth and follow her to the Eumi Island Temple to help her retrieving Manaphy. In order to get to Eumi Island Temple, go back to Eumi Island Town and then go west until you can see the entrance of the temple. Once you are in front of the temple, enter it. Once you are in the temple, interact with NPC Jyle and all the other NPCs will appear. From the temple, head back to Eumi Island Town and go to the docks, in Eumi Island Town. Once you're there, interact with Sailor Chip and head to the Temple of the Sea.
Temple of the Sea
When you arrive at the Temple of the Sea, interact with all the NPCs. After that, head north until you reach the Temple of the Sea Ground. From there, interact with the NPC, head north and defeat all the Captain Phantom's grunts. The average level of the Pokémon is 85. Once all the grunts have been defeated, head north, use the teleport pads and Captain Phantom will appear to fight you. He has a team of 5 level 100 Pokémon: Chatot - Pinsir - Dustox - Beedrill - Typhlosion. Once you have defeated Captain Phantom, the temple will start flooding and you have to escape. After you've escaped from the temple, Manaphy will run back into the temple and Lyzabeth will ask you follow it. From there, get back into the Crown room where you fought the Captain and search for the correct Jewel to place into the stone. Once you've found and placed the correct Jewel, get out from the temple and head south until you find Lyzabeth and her friends and talk to them. They will tell you that Manaphy's home is the temple and that it will go back there waiting for us. From there, go back another time into the Temple and reach the center of the map where you can find Manaphy ready to battle.
Tips and FAQ
- Can I synchronize Manaphy?
Yes, you can go back to take your Synchronize Pokemon before fighting Manaphy. In order to do that, simply talk to the Sailor and you will get teleported back to Eumi Island Town. As a tip, it is the best to bring a Timid Nature Synchronize Pokémon with you, and use Master Ball to be 100% sure about the outcome.
- Are there other ways to earn Manaphy?
Manaphy was a reward for the winner of Official Summer Tournament, one for each server (Silver-Gold). Also, each Manaphy was shiny-oriented and with great Individual Values.
- How can I get the X-mas Manaphy?
X-mas - oriented Manaphy was part of the Christmas Event and was available only from December 27th 2018 to 16th January 2019. Therefore, there is no possible way on obtaining it anymore.
- Can I change my X-mas Manaphy's sprite to the original sprite?
Yes, you can. Talk to Form Remover NPC in Eumi Island Theme Park 1 and he will change it for you! Remember, there is no coming back once you change it, so be careful.
- The server crashed / I defeated Manaphy. Can I somehow get another chance!?