Extra Stage Missions

[Sunflora Azumarill]

PRISM PYRAMID
Mission 2A: "What if all the robots were invisible?"
Unlocked: (--------------------)
Character: Rebecca
Upgrades Applied: Materia
On Radio: (-----)
Mission: Reach the Goal Gate.
Detail: If you remember going through this stage in Story Mode, you at times went through large halls with the walls being made entirely out of mirrors. Everything but the ceiling in these halls is invisible, and you had to look in the mirrors to see where everything is. Even the Team Rocket robots found here were invisible, including their attacks. Anyway, for this mission, all the robotic foes are invisible, making it much trickier to get through. Fortunately, Rebecca's laptop analysis allows you to indicate where the enemies are. You simply have to make it to the Goal Gate, which sits in front of the doors leading into the Crystal Clock. Once you go through the Goal Gate, the mission is cleared.
Challenge Mode: The Team Rocket guards are also invisible.

Mission 2B: "It's a Prism Pyramid Party, and look who's decided to crash it!"
Unlocked: Clear Mission 2A
Character: Duplica
Upgrades Applied: Tanks
On Radio: (-----)
Mission: Clear six of the numbers of the Crystal Clock.
Detail: In this mission, you're put into the Crystal Clock section of the stage. As it turns out, all of the villainous teams are present here and you must take six of them down. Each team occupies one of the number areas of the clock and consists of Grunts and equivalents for that team, robotic foes pertaining to them, two giants, and an Admin or equivalent for that team. Defeat all human foes in that puzzle to clear it. Here's the list of teams and their locations:

I: Team Magma, giants are Charizrard Jet and Magma Soldier, boss is Hank.
II: Team Aqua, giants are Empoleon Shield and Aqua Soldier, boss is Sean.
III: Team Flora, giants are Torterra Tank and Flora Soldier, boss is Peg.
IV: Team Plasma, giants are Mega Magnezone and Plasma Soldier, boss is Fargus.
V: Team Draco, giants are Salamence Jet and Garchomp Fighter, boss is thingy.
VI: Team Galactic, giants are Venusaur Tank and Metagross Walker, boss is Charon.
VII: Team Cipher, giants are Charizard Jet and Aqua Soldier, boss is Lovrina.
VIII: Team Snagem, giants are Torterra Tank and Plasma Soldier, boss is Wakin.
IX: Go-Rock Squad, giants are Slaking Soldier and Tyranitar Titan, boss is Tiffany.
X: Team Dim Sun, giants are Tyranitar Titan and Metagross Walker, boss is Kincaid.
XI: Team Rocket, giants are Cyber Aggron and Robo Rhydon, boss is Mondo.
XII: Miror B., giants are Dragonite Craft and Kingdra Cyclone, boss is Mirakle B.
The robotic foes inside Team Dim Sun's section consist of Ice-based Team Rocket robots, Sealeo Mechs, and Cloyster Shells in order to reflect the frigid environment on that puzzle.

Once you've cleared six number areas, the mission is clear.
Challenge Mode: You must now clear all 12 areas.

[Sunflora Azumarill]

GALAXY PARK
Mission 8C: "When did two colors get added to the rainbow water? I don't like the looks of this."
Unlocked: (--------------------)
Character: Ben
Upgrades Applied: Tanks
On Radio: (-----)
Mission: Get through Flashing Waters.
Detail: In this mission, you're put into the Flashing Waters area of the amusement park with pretty much the same setup. However, there's a major difference with the water. The unusual color-shifting water now has two more colors, teal (comes in between green and blue) and indigo (comes in between blue and violet). Teal water happens to act the same as frozen water (as seen in Crystal Glacier), which means that unless you're packing Thick Fat, you'll be frozen instantly. Indigo water acts the same as poison water (as seen in Flora Cave), meaning that you'll be killed instantly upon touching it unless you're equipped with Immunity. For this mission, Ben comes with two Ranger Signs, one for a Walrein (with Thick Fat) and one for a Zangoose (with Immunity). You can only summon one Pokémon at a time, but you can switch between them at any time in the stage. It's best to go with Walrein since that will allow you to swim in teal water, otherwise a three-color shift of yellow (immobilizes you), green (causes you to sink), and teal (freezes you) can easily seal your fate. A number of Team Aqua guards and robots make this mission a bit more difficult. Once you make it to the Goal Gate at the end of the area, the mission is clear.
Challenge Mode: Ben no longer has any Ranger Signs on him, meaning you get no protection from either teal or indigo water.

[Sunflora Azumarill]

CORAL TUNNEL
Mission 5: "Could it be that weird rainbow water flooding these coral lakes?"
Unlocked: (--------------------)
Character: Luka
Upgrades Applied: Chaos Drives
On Radio: (-----)
Mission: Swim through the flashing water.
Detail: In this mission, the water that is normally found in the stage has been replaced by the color shifting water from the Flashing Waters attraction of Galaxy Park. To remind you on each color of the water; red water damages you, orange water acts like gold water in Golden Plaza, yellow water makes you immobile, green water acts like Mega Mack, blue water is normal, and violet water reverses your controls. The color of the water shifts every five seconds in that order, so note that you should get out of there when it's violet before it goes back to red. To make things a bit easier, there are a few Clear Chaos Shards that can protect you from the red water. Reaching the Goal Gate at the end of the stage clears the mission.
Challenge Mode: A time limit of -:-- is in place. Additionally, Luka is wearing an Inhibit Belt and the Clear Chaos Shards have been removed.

[Sunflora Azumarill]

ELECTRIC PARK
Mission 5: "Make your way through the Plasma Card Complex!"
Unlocked: (--------------------)
Character: Dahlia
Upgrades Applied: Chaos Drives
On Radio: (-----)
Mission: Reach the Goal Gate.
Detail: In this mission, you're put into a place that is never visited normally in the stage, an area of the amusement park known as the Plasma Card Complex. This place is based off of Casino Street Act 2 from Sonic the Hedgehog 4 and consists of card-shaped buildings and other card-esque things like card paths, card platforms, and card arrays that work like those in Sonic 4. Various items are depicted on front of these cards. Flipping over four of the same item nets you that item. There are smaller cards that you can flip that can give you a number of Chaos Drives that are determined by the number of cards you flip. At some parts of the stage are card stacks and switches. Hitting these switches will cause the cards to slide out into a bridge for you to cross. There are of course Team Plasma guards and robots to watch out for. In addition to them, you also have a new card-like enemy called a Plasma Card, which only the front is vulnerable; the back is immune to attack. These foes fire electric shots shaped as red hearts, blue diamonds, green clubs, or yellow spades depending on the card. In the middle of the area is a large building made entirely out of large cards aptly called the House of Cards. This place is a maze and has switches that pull back or bring out some cards making up the walls, floors, or ceilings, allowing you to get through the House. Hidden in these walls happen to be Plasma Cards, so watch out. The final stretch of the mission is a long card bridge where the cards start to quickly retract, so quickly reach the other side and get into the Goal Gate to clear this mission.
Challenge Mode: The stage has been retooled to be as if in Expert Mode. One such change is there's now a Mega Magnezone inside the House of Cards.
Music Note: The Casino Street Act 2 theme from Sonic the Hedgehog 4 plays in the background for this mission.

[Sunflora Azumarill]

TROPICAL RESORT
Mission -: "EGGMAN: Hey Team Draco! What makes you think it's all right to freeze over my luxurious resort?!"
Unlocked: (--------------------)
Character: Clair (equipped Pokémon: Dragonair, Vibrava)
Upgrades Applied: Materia
On Radio: (-----)
Mission: Destroy all 15 Dragonair Controls.
Detail: In this mission, Team Draco's Dragonair Control robots have frozen over the entire area, making it snowy and frigid. As a result, there are some slippery sections in the stage and also snowbanks that slow you down and cause you to jump lower. Your mission is to destroy each of the Dragonair Control robots found in the stage. In addition to them, you're also contending with other Team Draco robots and Ice-based Team Rocket robots. Note that even though Abomasnow Titans and Castform Gauges (both of which are seen in this mission) cause hail as well, you only have to destroy the Dragonair Controls. Things can get very harrowing as Team Draco's Porygon-Z robots adapt to the weather in the area and hence pack ice abilities. You will come across Red, Yellow, and Cyan Wisps and Green, Blue, and Violet Chaos Shards in this stage that you can use to help you out or cross areas. Once all fifteen of the Dragonair Controls are destroyed, you clear the mission.
Challenge Mode: You must now destroy all of the Abomasnow Titans and Castform Gauges as well (there are 15 of each).
Music Note: The Tropical Resort Act 2 theme from the Wii version of Sonic Colors plays in the background for this mission.

[Sunflora Azumarill]

STARLIGHT CARNIVAL
Mission -: "EGGMAN: Princess Salvia, you seemed to have misplaced your Togekiss. Do you wish to reclaim it?"
Unlocked: (--------------------)
Character: Salvia (equipped Pokémon: Girafarig, Altaria)
Upgrades Applied: Tanks, Chaos Capacitor
On Radio: (-----)
Mission: Rescue Togekiss.
Detail: In this mission, Princess Salvia has apparently lost her Togekiss while touring Eggman's Incredible Interstellar Amusement Park (through an invitation he sent to her). You're put on a path not seen normally in the area, which you're going to have to traverse to reach Togekiss. Along the way, you'll be dealing with Eggman's robots and will come across Orange, Green, and Pink Wisps and Red, Teal, and Clear Chaos Shards (one area has you rocket into the air via Orange Wisp into a Teal Chaos Shard to jump even higher for instance). Eventually, you'll reach an area where you have to defeat a number of Eggman robots to open up an Eggman Cage holding Togekiss. Once the cage is open, simply go up to Togekiss, where Salvia will return it to its Pokéball, to clear the mission.
Challenge Mode: The Materia upgrades are in place instead of the Tanks and you no longer have the Chaos Capacitor.
Music Note: The Starlight Carnival Act 2 theme from the Wii version of Sonic Colors plays in the background for this mission.

[Sunflora Azumarill]

These three Special Missions are only unlocked once all other Special Missions are completed in both Normal Mode and Challenge Mode. If Tropical Resort and Starlight Carnival are unlocked before unlocking these missions, you must also clear the missions for those two stages. All three of these missions occur in the MechaMew2 boss arena.

BOSS STAGE: MechaMew2
Final Mission 1: "The Ultimate Challenge 1! The Rocket Storm!"
Unlocked: Clear all Special Missions in both Normal Mode and Challenge Mode
Character: Choice
Upgrades Applied: Tanks, Chaos Capacitor
On Radio: Prof. Oak
Mission: Defeat 2000 enemies.
Detail: In the first of the three Final Missions, you're going to be taking on every kind of foe from the entire game, plus several more. There are 2000 enemies total divided into 15 phases, with 133 or 134 enemies per phase. Each phase is divided into eight waves. Anyway, the phases are in this order; Team Magma, Go-Rock Squad, Team Aqua, Team Snagem, Team Flora, Dr. Eggman, Miror B., Team Dim Sun, Team Plasma, the Turks, Team Galactic, Team Cipher, Team Draco, Star City robots, and finally Team Rocket. Each phase is difficult, but from time to time, enemies will drop Potions and other powerups to help you out. Sometimes, enemies even drop Blue Chaos Shards you can use against them. The terrain also changes with each phase to make things more interesting. Once all 2000 enemies are down, you'll have cleared this mission.
Challenge Mode: There are now 3000 enemies to defeat with 200 per phase. Each wave contains around 25 enemies.

Final Mission 2: "The Ultimate Challenge 2! The Sub-Boss Frenzy!"
Unlocked: Clear Final Mission 1
Character: Choice
Upgrades Applied: Tanks, Chaos Capacitor
On Radio: Prof. Oak
Mission: Defeat all Admins and Equivalents.
Detail: In the second of the three Final Missions, you'll be taking on every Sub-Boss from the entire game, plus more. There are 66 total and healing occurs in between every group (i.e. a Potion in between Team Magma and Team Aqua). Anyway, here's who you'll be facing in order; Hank, Tabitha, Harland, Courtney, Sean, Isabel, Matt, Shelly, Tiffany, Clyde, Garret, Billy, Peg, Brad, Xenia, Seth, Butch & Cassidy, Carl, Sham, Annie & Oakley, Attila & Hun, Mondo, Wendy, the Rocket Scout, Jessie & James, Biden, Jedo, Wakin, Mirakle B., Reath & Ferma, Folly & Trudly, Fargus, Jack, Rhonda, David, Ice, Lavana, Heath, Kincaid, Hunter J, Domino, Ken, Al, & Harry, Megathug, Storc, Jagura, the Rocket Guardian, Charon, Mars, Jupiter, Saturn, Lovrina, Snattle, Gorigan, Ardos, Eldes, thingy, Murphy, Vikki, Rachel, Nanba, Proton, Pertel, Ariana, Archer, Sebastian, I.M.M., and finally Tyson (TR). The terrain will change to suit each fight and in some cases, you'll warp to the moon's surface or above it if that's needed to replicate the conditions for that battle. Once you've taken down Tyson, you'll have cleared this mission.
Challenge Mode: Healing now only occurs in between every two groups.

Final Mission 3: "The Ultimate Challenge 3! Ultimate Boss Match!"
Unlocked: Clear Final Mission 2
Character: Choice
Upgrades Applied: Tanks, Chaos Capacitor
On Radio: Prof. Oak
Mission: Defeat all the bosses.
Detail: In the final of the three missions, you'll be taking on every major boss from the game, plus four more. There are no items whatsoever in this mission, but you start out with a 5x X Health boost, a 10x X Defend boost, and a Max Revive. Here's who you will be facing in order, Maxie, Archie, Gordor, Farlie, Miror B., Gonzap, Plasmae, Blake Hall, Cyrus, Greevil, Dralene, Giovanni, MechaMew2, and of course finally, Hyper MechaMew2. Blake Hall and Greevil fight the same way they did in Pokémon Peace Squad 2 while Gordor and Gonzap fight the same they did back in Pokémon Peace Squad 3. The terrain will change to suit each battle and sometimes, you'll be warped to the moon's surface or above it if that's needed to replicate the conditions for that battle. When it comes to facing Hyper MechaMew2, you'll watch a short cutscene of your character using the Super Emeralds to go hyper before you head out to fact it. (Find Your Own Way orchestrated starts playing when this battle begins and Mewtwo in its Hyper form still assists you during the fight, including you switching over to it when you normally do.) Once Hyper MechaMew2 is defeated, this mission is cleared.
Challenge Mode: You no longer have a Max Revive, meaning you truly have only one life in which to do this mission.