The story begins:
Shock wakes up and realizes he and his Pokemon Shinx are late to begin their journey. His friend/rival Flame and his partner Fennekin are waiting, understandably angry. Shock and Flame often bicker, and so do their Pokemon.
Flame is from Kalos, and moved to Sinnoh. Shock has always lived in Sinnoh. Flame found Fennekin after she escaped from Team Magma in the Hoenn region, where she was being used as a weapon, and Shock found Shinx after he was injured by a truck.
Shock and Flame leave Shock's house, narrowly escaping Shock's mom's meltdown. They head through Eterna City to a newly installed Pokemon lab where they talk to Professor Maple and get their Pokedexes. She informs them of the gym leaders, who they plan to defeat along their journey.
They head south to route 206 on their way to Oreburgh. On their way, they battle their first Pokemon and Flame catches a male Shroomish which he names Shroom.
They also pass through a cave in which they battle Zubat. They find a note on the floor reading: Come to Celestic Town. Possible lead on Diamond/Pearl there! Bring strongest Pokémon. ~ Midnight. Shock realizes this must mean Dialga and Palkia, so they plan to go there at some point after they beat the first gym. They arrive in Oreburgh and watch a battle going on in the gym. They decide to train more after seeing such an intense showdown, so they head to route 203 to battle some Pokemon.
They split up and decide to meet later and have a battle. Flame hurts his ankle, making him unable to move quickly, though he still manages to train. Fennekin spots an Abra, and Flame tries to catch it, but it teleports away. He trains Fennekin and Shroom more, battling trainers on the route. Meanwhile, Shock and Shinx are also training, growing more powerful and fighting trainers. Flame and Shock find each other by accident in the woods, and decide to train together for a while.
They spot a group of four people walking through the woods in dark clothes. They have an "SF" emblazoned on badges they wear. The people spot them and attack. Shock and Flame try to fight them but are overpowered, so they attempt to run away. Flame's hurt ankle is slowing them down and the people are gaining on them, but a Starly appears and distracts them long enough for Shock and Flame to escape with their injured Pokemon.
The Starly returns to them after escaping the sketchy people, so Shock decides to catch it. It is female, and Shock names her Aero. Realizing they might be too weak still, Flame and Shock split up again after healing their Pokemon in order to train even more. Shock catches a female Sneasel who he names Frost. He decides to keep her a secret until the gym battle so she can make an epic entrance.
After a bit more training, Flame and Shock meet up again for their battle. Shock barely manages to win the battle without Frost by using Aero's type advantage on Shroom.
They debate whether or not the note has to do with the sketchy people in the woods, but decide it would be too much of a coincidence. They learn that their Pokedexes can make phone calls, so they contact Professor Maple and ask about people with a badge reading "SF." She tells them that they have been seen all around Sinnoh, causing trouble. They always seem to be searching for something as well.
Shock and Flame decide to keep an eye out for the SF people, then make a trip to the Pokemart to stock up for their gym battles.
The next day they head to the Oreburgh gym to fight Roark. They make their way up a rock wall, and Flame decides that he will have the first battle. He barely wins the fight, making use of Shroom's leech seed and Fennekin's flame charge and blaze ability.
They head back to the Pokemon center so Flame can heal his Pokemon, then make their way back to the gym for Shock's battle. Shinx and Aero are both knocked out in the battle, but at the last second he reveals Frost, his Sneasel. He used a ™ to teach Sneasel brick break, which he uses to win the battle. They now each have the Coal Badge.
Since they've beaten the Oreburgh gym, their next destination is Celestic town. In order to reach Celestic town, they have to pass back through route 206 and Eterna City. On their way back through Wayward cave to Eterna, they see a group of SF people running by. They hide from them, but one of them drops another note which reads; "Celestic locked down. Citizens resisting, bring backup."
Seeing this, Shock and Flame start to hurry to Celestic town. They briefly visit Flame's family in Eterna, deciding they'd better wait to do the gym battle there until they've been to Celestic to at least see what's going on, then make their way to route 211. On the route, they battle a few Pokemon, and Aero evolves into Staravia. They pass through a part of the caves under Mt. Coronet, and see more SF people running back and forth through the area. They avoid most of them, but are forced to battle a few. They win, but just barely, so they heal up their Pokemon and continue on their way.
When they emerge from the cave, Flame catches himself a Helioptile that was taking their snacks. He names him Helios.
Shock and Flame both train their Pokemon a bit more, knowing that they'll be facing a fight in Celestic. Shinx evolves to Luxio, and Fennekin evolves to Braixen and reveals her crippling stick addiction. Shock also finds out that Frost is very lazy.
They decide it is time to go into Celestic town. There are still SF people swarming over the route, heading in and out of the town, so they sneak past most of them. They battle a few guarding the entrance, winning with relative ease, and make their way in.
The town is filled with SF people. They are coming in and out of a cave at the center of the town and there are guards stationed everywhere. The citizens seem to be trapped inside, although a few trainers are trying to take back their town. The numbers are too great, however, so there is hardly any hope of them actually defeating all of them.
Curious about what's going on, Shock and Flame manage to battle their way to the cave, where they are able to sneak in. Inside, there are many people chipping away at the walls, carving out a tunnel through the earth.
Shock realizes that this is the cave in which there are supposed to be etchings of three legendary Pokemon, Azelf, Uxie, and Mesprit. They scan the area for those etchings, but decide that the SF people must have destroyed them in their mining. They wonder if the cave might also have some connection to Palkia and Dialga, considering the earlier note, but they can't be sure.
They can't see him from their hiding place, but someone who seems to be of a high rank among the SF group begins to give a speech. The others refer to him as "Midnight," which is the exact name of the author of the first note they found in Wayward cave.
Midnight calls his people the "Shadow Force," which explains the SF badges they all wear. He then talks about underground ruins rumored to be hidden beneath Celestic that reveal how to obtain Diamond and Pearl, which Shock and Flame assume means Dialga and Palkia.
He mentions finding something called "Null" and that there are people searching everywhere, although the two hiding trainers have no clue what he's talking about.
Before they can learn any more of the Shadow Force's plans, they are spotted and attacked. Midnight looks on as they struggle to battle against the countless Shadow Force soldiers. Before long the two have been overwhelmed, all of their Pokemon defeated. Midnight orders his soldiers to kill them.
Before they can be killed, a woman fights her way into the cave, defeating many soldiers with her Garchomp. Shock and Flame's captors are distracted, allowing them to escape. Running from the cave, they see that the town has been cleared of Shadow Force soldiers. They hide close to the cave entrance, waiting to see what happens.
They see Midnight exit the cave and send out a massive Pokemon (Golurk) and fly away on top of it. Many Shadow Force soldiers follow, jumping on various flying Pokemon. The woman leaves after them, sending a final attack into the sky, which is dodged.
Shock and Flame come out of hiding, and the woman introduces herself as Cynthia, the champion Pokemon trainer of Sinnoh who has grown much older since Team Galactic was destroyed. Her family lives in Celestic town, so she was coming to visit and saw that the town had been locked down by a bunch of evil looking people. As one would, she wrecked all of them and finally entered the cave, saving Shock, Flame, and their Pokemon.
Shock and Flame thank her for saving them, and tell her what they learned about the Shadow Force's plans. Cynthia hears of the underground ruins and tells the two young trainers the story of the sacred place.
The underground ruins were originally a sacred place for tribes that lived centuries before the invention of pokeballs, but when those tribes died out the ruins became abandoned. Years before the battle with Team Galactic about 20 years previously, Cynthia discovered a hidden passage a little ways up Mt. Coronet. She entered it, and learned it lead to a massive cavern located directly beneath Celestic town. Within the cavern was the ruins of an underground city, completely deserted. She kept the information from everyone but her closest family members to protect the ruins from thieves that might try and loot the place, effectively destroying the once sacred ground.
When the battle with Team Galactic came and Cyrus created the red chain, he did not know of a second red chain that was created. The red chain is an incredibly powerful item which can be used to summon and control the two legendary Pokemon, Palkia and Dialga. To prevent the dangerous item from falling into the wrong hands, Cynthia hid it away in the underground ruins. She doesn't know how Midnight learned of the location of the red chain, but she realizes that she needs to move it before it is found by the Shadow Force.
Saying goodbye to the two trainers, she heads to the ruins after checking in with her family. The citizens of Celestic are beginning to recover, so Flame and Shock get their Pokemon healed before heading back to Eterna for their second gym battle.
They contact Professor Maple and tell her about what they learned. She informs them that more of the Shadow Force are appearing around the region. Some are at the three lakes, Acuity, Verity, and Valor, presumably searching for Uxie, Mesprit, and Azelf. Others are swarming over the whole region, looking for a so called "Null," although nobody recognizes the name. The police and trainers of the region are fighting back, attempting to drive them away, but the Shadow Force is resilient. They refuse to reveal their origin or what their plans are.
Hearing this, Shock and Flame decide to become as strong as possible to help Cynthia and the region fight off the Shadow Force. Shock and Flame split up briefly to check in with each of their families after they both just almost died, then meet up again to do some training to battle the Eterna gym leader Gardenia.