Unlocking the Extra Missions
In order to unlock the Extra Missions you must first finish the game's main storyline by successfully completing all ten of the main Ranger missions. You do not need to finish the side missions to unlock the Extra Missions. After stopping Gordor and defeating Raikou, Suicune and Entei, a cut scene will begin, followed by the credits. Your game will automatically save and you will start again from the title menu. Begin your saved game and the Extra Missions will now be available.
Special Mission 1: Search the Safra Sea!
When you start the game again, you will once again be in Fall City. Talk to Professor Hastings at the Lab with no partner Pokemon in your party. He will ask you to meet Joel at Fall City's Base. Agree to help to begin the mission. Joel will tell you that there is a disturbance in the sea and ask you to investigate. After helping several scared Pokemon you will encounter the source of the disturbance -- the Legendary Pokemon Kyogre.
Special Mission 2: Summerland Rescue Duo!
After completing the first Special Mission, talk to Spenser at the Base in Ringtown with no Pokemon in your party. He will ask you if you are tired, to which you must reply "Yes" to begin the mission. He will take you on vacation to Summerland. When you reach your destination you will be asked to look for a missing Pokemon Ranger. After exploring the area and encountering fire Pokemon and a Go-Rock Grunt, you will come across, and rescue, the Legendary Pokemon Groudon.
Special Mission 3: The Temple's Sinister Shadows?
The final extra mission is given to you by Elita outside of the Base in Wintown when you talk to her with no Pokemon in your party. She will ask you if you want to complete a special mission and investigate the Fiore Ruins. Agree to help her and you will team up with a Ranger named Chris to find out what is happening in the ruins. After confronting several Go-Rock Grunts you will encounter and capture the final Legendary Pokemon, Rayquaza.