After the end credits, you find yourself back at Ring Town, and your fellow Ranger's partner pokemon (Plusle or Minun), will add its data to your Ranger browser. Hayate tells you that you are qualified to take pokemon out of their habitats, and I'm sure you would have noticed many obstacles in areas which cannot be cleared by the local pokemon, so find your way around to clear them, because behind those obstacles almost always hold pokemon that you have not captured before, and are essential to complete you Ranger Browser. Revisit old places as well, because many new ones are added after the end credits, and the Lila Forest and Olive Jungle are good places to start with.
Certain pokemon can only be found in the Field or Sea Capture Challenges, and some are unlocked by special means. Check the Capture Challenge pages to find out more about them. But to continue the story, head to Fall City next.
Talk to Prof. Shinbara, and he will request you stay overnight to discuss things with him. The next morning, his assistant comes in and informs you that something is wrong in the Saffra Sea off the shore of the harbour. Prof. Shinbara tells you to go investigate, and you start your first special mission.
Special Mission 1: Investigate Saffra Sea's Mysterious Change
Aria will accompany you on this mission, and odd things will start to happen around the harbour. The first thing you need to do is head down that flight of stairs where you found a Staryu before. You need to capture 4 ramapging Staryus this time though, so be prepared. After that, you hear screams from the small ticket house on the left, and you head in to capture 4 rampaging Krabbies. Following that, head to the shoreline, and there are also 4 rampaging Carvanhas waiting for you to tame.
Afterwards, people will alert you to some big whirlpools out in the Saffra Sea, and you decide to ride on Lapras to investigate. However, you soon get sucked into a whirlpool, and you end up face to face with the ancient sea titan, Kyogre. This might be a bit tough because from the beginning of this mission, there are no means to charge up your Styler, and technically there are no pokemon to recruit for assistance either. Plusle/Minun is the only one you can count on, and if you've used up its energy bars on the Staryus, Krabbys or Carvanahas, you have to charge it up again yourself by circling Kyogre.
So, Kyogre technically isn't the most difficult pokemon to capture. It rarely attacks, and only causes giant waves to wash across the screen every now and then. Avoid those waves, and quickly circle around it, and you should be able to capture it. After you do, head back to the Ranger Base and your mission's complete.
Next, go back to Ring Town to talk to Hayate, and he'll want you to help you other special missions. He tells you to head to Summer Land, and Summer Land you go. Once you're there, Kamuri will tell you that something is wrong at the Jungle Ruins and the weather is getting increasingly hot. He remarks that your fellow Ranger has already gone off there to investigate, so off to the Jungle Ruins now.
Special Mission 2: Save Summer Land With Two People's Efforts
Once you're inside the Jungle Ruins, find your way around to the cave where you found Poliwhirls and Poliwraths before. There will be a boulder there blocking the way, and your fellow Ranger's partner pokemon will be unsettled. Apparently your fellow Ranger is trapped inside, so get a Rhydon to clear the obstacle.
Once you join your partner, get a Poliwrath for obstacle clearing later, and one more to for pokemon assist later on. Head north, clear the lava plague with one Poliwrath, and fight a Team Go-Go member with two Metangs. Venture deep into the ruins, and in the same room where there are Charmeleons, drop down the hole and you will soon find yourself face to face with the ancient land titan, Groudon. Again, Groudon isn't really that difficult to capture, especially if you have Poliwrath's Water type pokemon assist to trap it in a bubble temporarily.
Capture Groudon, and your fellow Ranger will remark that it seemed to have been fighting with Kyogre not long ago, and that both titans seem to have been awakened by someone. Anyway, you mission here is complete, so head back to the Summer Land Ranger Base.
Now that two titans are settled, go to Wint Town for the last one. Erida will be waiting outside the Ranger Base, and tells you of weird sightings near the Fiore Temple lately. Her Ranger Kres comes along with you, and off to the Fiore Temple you go.
Go up, and you will first fight a Team Go-Go member with a Solrock and Swellow, then another one with a Houndoom and 2 Donphans. When you get to the top, you see Team Go-Go members failing to gain control over the ancient sky titan Rayquaza, and it's clear that all the titan fuzz were started by these Team Go-Go remnants.
Anyway, challenge Rayquaza, and if you have Glalie to freeze it or Gengar to stump it, it shouldn't be a difficult task. Kres will be very impressed by your skills after you do so, and calls you the legendary Ranger. Head back to Wint Town, and your mission's complete.
Technically all the ingame missions are complete at this stage, and what you need to do next to capture all 210 pokemon species in Fiore. You might have noticed by now that the sleeping Snorlax you see throughout the game has taken a permanent residence in a cave at the Cycla Mountain Ranger. But until you have captured the other 209 pokemon, it will not awaken. Once you capture Snorlax as well, Hayate will message you to head back to Ring Town. There, the final animation is shown which everyone congratulates you for being the first ever Ranger to complete the Ranger Browser. With that, a Completion Emblem is rewarded to you on your Ranger card, and you have beaten the game.
The rest of the game must be unlocked via events, including the Deoxys mission, which takes place at the Croca Tunnel, and the egg of Manafi, which seems to involve the Summer Land, Lila Forest and perhaps more.
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