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Pokémon Mystery Dungeon: Explorers of Time & Darkness (Japanese: ポケモン不思議のダンジョン 時の探検隊・闇の探検隊 Pokémon Mystery Dungeon Time Expedition & Darkness Expedition) is a special based on Pokémon Mystery Dungeon: Explorers of Time & Explorers of Darkness.
Inside a cave, a Grovyle found a glowing item, the Time Gear. Grovyle takes the item and sees time has stopped in certain places, then moves away. Elsewhere, a Chimchar has arrived to a tent called Wigglytuff Guild. Chimchar hopes to be famous by working for the guildmaster. Chimchar comes into the tent, but a recent blast causes him to go to the ceiling, as a Zangoose, a Scyther and a Sandslash were blown off. Corphish claims these three Pokémon, Team Razor Wind, lost and have to obey the guildmaster's wishes, with Chatot taunting them. A Diglett notices some footprints and claims a Chimchar has stalked in here. Chimchar is afraid and runs off, then trips over a Piplup. Chimchar wakes Piplup up, who does not know where he is. Piplup is terrified, as Chimchar can talk. Piplup pinches himself, but sees this is no dream.
Chimchar considers Piplup strange, but funny. He asks Piplup where does he come from, but Piplup does not recall. Anywhom, Piplup claims he is a human, but sees his reflection in the bubbles, realizing he is a Pokémon. Chimchar proposes Piplup could join his exploration team, to find hidden treasures and defeat many bad guys, even rescuing other Pokémon. Piplup refuses, since he has to find out what happened to him. To help out, Chimchar takes Piplup to Wigglytuff guild, as the guildmaster may know something about Piplup's "condition". Suddenly, they are startled by Diglett, who claims there are intruders about. Chimchar and Piplup fall into a pit and are being taken to guildmaster Wigglytuff. Piplup, despite other Pokémon's disapproval, talks with Wigglytuff, clarifying he was a human that woke up as a Piplup. Wigglytuff considers this odd and falls asleep, with his eyes open. Chimchar considers this a worthy trait.
Chatot explains Wigglytuff meant to say is that many strange things have been happening and more bad-willed Pokémon have been sighted and cause trouble. The graver is the fact is that the Time Gear has been broken, causing the balance of time to be disturbed. Wigglytuff wakes up and asks Chimchar and Piplup a name for their exploration team. Chimchar replies "Poképals", as he thinks being friends with others is an important thing. Wigglytuff approves and uses Hyper Voice, affecting all Pokémon, for it was a ritual to create this new exploration team. Sunflora gives Chimchar and Piplup an exploration kit, as well as two badges. During the night, Piplup is thinking about certain events. Chimchar, who is asleep, rolls to Piplup's side. Piplup tries to lift Chimchar away, but has a vision of two Kecleon merchants wanting to sell him, Chimchar and a Sunflora some items.
Next day, after an inspirational speech from Chatot at the guild, a Shinx comes to the guild, asking for a Gabite scale for his sick sister, which has antidote properties. Wigglytuff thinks this is Poképals' first mission - to retrieve the Gabite scale. Wigglytuff gives them the directions to the Labyrinth Cave. Chimchar is shocked, as that cave has many corridors and inside the powerful, fierce Gabite, lives. Wigglytuff has Sunflora join Team Poképals, who is glad she can join in the adventure. Corphish considers Sunflora an expert in exploring. Later, Team Poképals go through the village and find the Kecleon brothers. Sunflora goes to shop for some items they may need for the Labyrinth Cave. Team Razor Wind observes them, making Zangoose think Chimchar, Piplup and Sunflora are just rookies for the Labyrinth Cave. Piplup recalls his vision, seeing it came true that Sunflora was buying stuff from the Kecleon brothers.
Sunflora tells the wearer of the Joy Ribbon receives more experience, while the Defense Scarf boosts defensive powers and the Power Band increases attack. Later, Team Poképals enter the Labyrinth Cave and get attacked by Golbat. Sunflora uses Razor Leaf, dismissing the Golbat, who fly off. Chimchar thanks Sunflora for saving them. Sunflora is flattered, but reminds them they have to receive the Gabite scale for Shinx. Piplup walks and nearly falls down the cliff, but Chimchar grabs his arm. Piplup has another vision of the cave collapsing. They soon come to two bridges, though the bottom is too deep. Chimchar goes to cross the stone bridge, but Piplup pulls him, fearing for his life, proposing to take the log bridge. Chimchar is annoyed, but the cave shakes and the bridge collapses. Chimchar and Sunflora are shocked, but thank Piplup for warning them in time, who doubts he should tell them he saw it in the vision.
As Team Poképals continue, they encounter Team Razor Wind, injured. Sandslash replies they were attacked by Gabite. Scyther reports they wanted the Gabite scale, but Gabite claimed they had to fight for it and were attacked. Zangoose doubts they'll do better, since they are just rookies. Chimchar and Piplup remember Shinx's request and do not plan on retreating. They walk into the cave, where they see Gabite. Team Poképals ask for the scale, but Gabite refuses, since he has always given away the scales. Gabite does not care, even if it is to heal Shinx's sister, but promises to give it away if Team Poképals defeat him in battle. Piplup, Chimchar and Sunflora have no choice and accept the challenge. Gabite starts with Sand Tomb, so Chimchar uses Ember, but nothing happens. Piplup uses Bubble, stopping the Sand Tomb.
Gabite uses Dragon Claw, striking Chimchar and Piplup. Sunflora uses Razor Leaf, hitting Gabite. Sunflora attempts to use Petal Dance, but is affected by Gabite's Attract, thinking of him as a charming Pokémon. Piplup uses Peck, hitting Gabite. Piplup uses Bubble, though Gabite evades the attack and retaliates with Dragon Claw. Gabite goes to attack again, but is hit by Chimchar's Fury Swipes. Piplup uses Bubblebeam, a move he learned recently, due to Joy Ribbon. Piplup repeats the attack, hitting Gabite. Gabite attempts to attack again, but falls in defeat. Sunflora's effect is dispelled and noticing Gabite defeated, congratulates Chimchar and Piplup on teamwork. Gabite stands up and gives them his scale away, since that was a good battle. Sunflora commends them on the success of the mission, since they have obtained the scale.
Shinx thanks Team Poképals, for his sister has been healed. For a reward, Shinx gives them a Luxray fang. Chimchar goes to take it, but Chatot snatches it, reminding them the rules of the guild are that the rewards go to the guildmaster himself. Chimchar and Piplup are displeased, even if that are the rules. Loudred and Corphish arrive, reporting another Time Gear has been stolen, the thief being Grovyle. Piplup decides to remain with Team Poképals, for there are many Pokémon out there needing their help, and may be steps closer to discovery what happened to him. Chimchar is glad and shakes hands with Piplup for future cooperation.