After a bit of battling wild Pokemon, they head to the gym. The inside of the gym is basically a forest, so they have to find their way through the maze of trees to the gym leader. When they reach her, they learn that they can do a double battle. Gardenia brings in a trainer from her gym, while Shock and Flame decide to fight together.
Frost and Braixen do a good job taking out one Pokemon each, but are defeated by the second. Helios and Luxio take down the two already weakened enemy Pokemon, then are defeated by Gardenia and the trainer's last Pokemon Each. Aero and Shroom come out against the enemy Roserade and Cherubi. Aero takes out the Cherubi, but is tied down by Roserade's grass knot and beaten by magical leaf. Now it is just down to Shroom. Shroom is beaten to his limit, until he finally evolves and wins the battle with his new lightning fast punches as a Breloom.
Soon after completing their gym battle and getting the forest badge, the two receive an urgent call from Cynthia. She tells them that Midnight and a few members of the Shadow Force are already in the ruins, and that she's trying to hold them off. Unfortunately, Midnight is about equal to her in strength, and he's got backup. She has already called the elite four to help, but they are far closer and will most likely get there more quickly. She warns them that the Shadow Force is showing no mercy.
The two trainers decide to go and help her, so they set off for Mt. Coronet. Cynthia gave them basic information on where the entrance to the ruins are, but they have a rather vague idea of where to look. They pass through part of route 211, and then instead of passing through the cave, start making their way up Mt. Coronet. After several hours of hiking, they begin to worry that Cynthia has been defeated, but remind themselves that she has been the champion for more than 20 years. She took a short break when a boy called Lucas defeated her, but he disappeared shortly after. She then took back over as champion, and remained in the position until the present day.
Shock catches a Rockruff he names Quake, and Flame catches a male Fletchinder he names Talon. They soon reach a small opening in the side of a cliff which they believe is the entrance. To make sure, they try to call Cynthia, but they have no signal. With no choice, they enter the cave.
Using Luxio's claws and Braixen's flaming stick for light, they make their way through the narrow passage. They begin to see light and the sounds of a battle. Hurrying, they run towards the light. They emerge into a massive cavern filled with broken down buildings and pillars and temples and shrines. Atop a huge podium lay a red chain. They could see Midnight and a few SF soldiers preparing to grab the chain and leave, then noticed Cynthia hiding behind a pillar holding an ultra ball about 100 meters away. She sees Shock and Flame, and seeing that she has reinforcements (although it isn't a group of the most powerful trainers in the region, but two twelve year old,), leaps from her hiding place and sends out a Lucario. Lucario begins to clash with a Zoroark sent out by Midnight while Shock and Flame each begin to take on SF soldiers.
Shroom and Frost's fighting type moves work well against the SF soldiers dark types, making up for the superior levels, but they are still greatly outnumbered. They look back to Cynthia, seeing her Garchomp locked in combat with Midnight's Tyranitar. Before long Shock and Flame are being overwhelmed once more. Cynthia's Milotic is snaking around Midnight's Golurk, confusing it and hitting it with water attacks, while the two young trainers are down to their last Pokemon. They learn that SF soldiers are delaying the elite four, keeping them from helping the champion and saving the Red Chain.
Shock and Flame's Pokemon have been defeated. They run to find a hiding place among the rubble and use their potions. With Luxio and Braixen healed, they prepare to continue the fight. Luxio takes the moment to evolve into Luxray, giving them a better chance. Before they can rejoin the battle, however, the elite four descend into the cavern. Midnight sees this, has his Golurk grab the red chain, blasts a hole through the roof, and flies out. His soldiers follow him. Cynthia gives chase atop a Togekiss, while each of the elite four flies after her. Aaron on a Yanmega, Bertha on a Gliscor, Lucian on a Xatu. Shock and Flame each hitch a ride on Flint's Charizard.
An airborne chase begins. The flying Pokemon battle with the SF soldiers, trying to catch up to Midnight and his Golurk. Flint's Charizard blasts fire at its enemies, leaving Shock and Flame in awe of its power. While the elite four battle Pokemon such as Honchkrow and Mandibuzz, Cynthia engages in a fight with the now flying Golurk. Flame asks Flint to get them close enough to jump onto Golurk, and seems to have a plan.
Flint takes out his enemy, then flies them as close as possible to Midnight's Pokemon. Flame leaps through the air and just barely manages to grab the massive Pokemon. He climbs up the side and tries to grab the red chain, which Midnight is now holding. The SF leader is startled and almost loses his grip on the powerful item, but at the last second pushes Flame hard enough that he falls off of Golurk completely.
Shock watches, time seeming to slow. He jumps from the Charizard without warning, sending out Aero. He and his Pokemon dive towards Flame, who has gone completely unconscious. Just before they reach the ground, Aero evolves in mid air, catching them both.
While all of this was going on, Cynthia and the elite four dove after them, attempting to catch them in time. In doing this, they left Midnight alone to escape. They had lost the red chain.
They all return to Celestic town to regroup. They do not know what Midnight plans to do with the power of Dialga and Palkia, but they know they need to stop him. After Shock and Flame's near death experience for the second time, Cynthia tells them to train hard and defeat the gym leaders so they can be stronger if they meet the Shadow Force in battle again. They agree, and they all go separate ways. Cynthia is going to research Dialga and Palkia, while the elite four are returning to the Pokemon league.