Ash and his friends join Brandon in his flying Battle Pyramid and head for Snowpoint Temple, where something sinister is afoot. Legend says that long ago, Regigigas, Registeel, Regice, and Regirock saved Snowpoint City from destruction. Registeel, Regice, and Regirock then transformed into the pillars of Snowpoint Temple to protect Regigigas, who still sleeps within. Now, Pokémon Hunter J and her minions have invaded the temple to catch Regigigas; when they see the Battle Pyramid approaching, they send swarms of Pokémon to attack, forcing the Pyramid to make a crash landing! But with the help of their Pokémon, our heroes make it past the swarms and into the temple—too late! J has just destroyed the temple's three pillars, rousing Regigigas from its slumber.
Furious at being awakened, Regigigas starts to attack everything in its path. It emerges from the temple and continues its rampage, so Brandon has his own Registeel, Regirock, and Regice battle it: if he can capture it, that might calm it down. But as Brandon prepares to throw his Poké Ball, J snares everyone in Ariados’s webs and tries to catch Regigigas herself. Her failed attempt only makes things worse: now Brandon's Registeel, Regirock, and Regice won't return to their Poké Balls. Instead, they join Regigigas in its march of destruction!
J and her minions reassemble to try and trap the advancing Pokémon in a canyon. Once they have Regigigas snared in a sticky trap, J moves in for the capture, but Registeel, Regirock, and Regice leap to Regigigas's defense and are hit by J's special freeze rays. Ash and his friends get there just in time for Brandon to intercept J's next attack, but now Brandon is frozen too! All the commotion causes J's clients to cancel their request, so J and her men retreat. Regigigas calms down and unfreezes Brandon and his Pokémon before it returns to its slumber. Brandon promises to protect Regigigas: not only will he and Maria fight to defend it, his own Regice, Registeel, and Regirock will guard Regigigas by becoming the new pillars of Snowpoint Temple.
Maria and Samuel arrive with the news that "a mysterious group of people" have sealed off the Snowpoint Temple. Brandon orders Maria and Samuel to board the pyramid so they can go to the temple and see what is going on. Ash, Brock, and Dawn insist on going too, and Brandon consents. Team Rocket, around the corner of the pyramid, overhear and decide that they will tag along. The Battle Pyramid takes off, with Team Rocket holding on.
Inside the pyramid, Brandon asks Ash if he has heard the legend of the Snowpoint Temple. Ash says he would like to hear it, and Maria begins. Long ago, there was a violent volcanic eruption that turned the once-beautiful Snowpoint Forest into a sea of lava. Out of a bright blue light, Regigigas appeared with the legendary titans. The four stopped the volcanic eruption, saving Snowpoint City. Afterwards, Regigigas went into a deep sleep in the Snowpoint Temple, protected by Regirock, Regice, and Registeel, who had transformed into guardian pillars. Brandon guesses that the mysterious people are after Regigigas. Meanwhile, clinging to the pyramid, Team Rocket overhears and decide to capture Regigigas for Giovanni. In their excitement, they accidentally let go and blast off.
Samuel shows the entrance to the temple on a screen, revealing a figure whom Ash recognizes as Hunter J. Brandon tells Maria and Samuel about J, also telling Ash and friends that he is here to do research on the legend, which has basis in fact. As Ash presents the idea of stopping J from catching Regigigas, J's henchmen see the Pyramid and inform J. J orders her henchmen not to let the Pyramid get near, and they send out a virtual army of Metang and Skarmory to attack the Pyramid with Sludge Bomb and Flash Cannon, respectively. One of the engines is hit, forcing an emergency landing. Brandon, Maria and the gang leave in a small airship, while Samuel stays to repair the Pyramid's motor. The henchmen notice the small craft, and order their Pokémon to attack, but the gang is saved by Pikachu, who uses Thunderbolt on the Skarmory, and Piplup, who uses Bubble Beam on the Metang. After defeating the Pokémon, Brandon, Maria, and the gang run into the temple.
Meanwhile, J has reached the three pillars and sends out Salamence, commanding it to destroy them with Hyper Beam. The ice and rock pillars are easily destroyed, and, just when Salamence is about to destroy the steel pillar, Brandon yells for J to stop. Maria explains that awakening Regigigas is a bad idea, but Salamence destroys the steel pillar anyway. A small blue ball between where the pillars once stood has begun to glow, but, other than that, there is no sign of Regigigas' awakening. J commands Salamence to use Flamethrower, much to Brandon's dismay. Suddenly, a triangle on the floor that had connected the pillars begins to glow, and Regigigas appears, immediately using Hyper Beam on the temple's walls and ceiling. J prepares to turn Regigigas to stone, but Regigigas stops her with Hyper Beam, forcing Salamence to counter it with Dragon Pulse. J retreats while Regigigas goes on a rampage. As the temple starts to collapse, Brandon sends out his Regirock, Regice and Registeel. The titans save the gang from being buried in falling rock by using Focus Punch, Zap Cannon and Flash Cannon, respectively. The gang escapes, protected by the titans, right before the temple collapses into a pile of rubble. Just when Brock notes that Regigigas cannot escape the rubble, it suddenly breaks out, still shooting Hyper Beam in every direction.
Brandon decides to calm Regigigas down by attempting a capture. His titans use Hyper Beam, but Regigigas counters it with a Hyper Beam of its own. The titans then charge Regigigas to use Focus Punch together, but Regigigas pins them down. Regirock and Registeel then grab onto Regigigas, and Regice uses Ice Beam, freezing Regigigas along with Regirock and Registeel.
J is watching, smiling darkly, happy that they are weakening Regigigas for her. When Regigigas defrosts, Regice uses Zap Cannon, paralyzing it. Registeel uses Iron Head, knocking Regigigas to the ground. Regirock uses Stone Edge, weakening Regigigas even further. Brandon prepares to capture Regigigas with a Poké Ball, but just before he throws it, J's Ariados uses its String Shot to tie him up, along with the entire gang. J returns Ariados to its Poké Ball, while Regigigas' eyes begin glowing, followed by the eyes of the titans. Confuse Ray takes effect and, as in the legend, the titans become Regigigas' guardians, attacking J (Regirock and Regice with Zap Cannon, Registeel with Flash Cannon). The four legendary Pokémon then begin to leave the temple together, and J follows.
All four start to attack the mountains with Hyper Beam. Brandon tries to stop them, failing. He then tries to return his titans to their Poké Balls, but they are not responding to him at all. Regice then turns on Brandon, using Zap Cannon, but Brandon is able to dodge it. Dawn notes that the four legendary titans seem to be heading for the city… it could become a catastrophe if they reach it.
The legendary titans continue using Hyper Beam once in the forest. Team Rocket still has a plan to capture Regigigas, but Registeel blasts them off using Flash Cannon. Back by the temple, Piplup tries to chew through the web binding Dawn while Brandon, Ash and Pikachu struggle to break free of their ties. Brock, stricken with love for Maria, tells her that he is happy to be with her and he would never let go of the web that tied them together. Dawn questions Brock's timing as being completely inappropriate due to their situation, but then Croagunk comes out and uses Poison Jab on him; the attack breaks the web and Ash and Brandon commend the pained Brock on his quick thinking. Soon free, the gang is back in the mini-airship. Brandon checks in with Samuel, who says he needs more time to finish repairing the Pyramid. Brandon tells him to tell Officer Jenny to be on the alert while he catches up to Regigigas.
Meanwhile, J has gotten ahead of the four legends with her airship, ready with her henchmen to catch Regigigas. When the four legendary titans reach J, her airship shoots lasers at them, which the legendary titans counter with Hyper Beam. Afterwards, the airship shoots a liquid adhesive, which bears a striking resemblance to bubble gum, at Regigigas, to trap it. Regigigas is not completely immobilized by the gum, however, and uses Hyper Beam to destroy one of the airship's engines. While dodging Hyper Beams fired by the three titans, J orders her henchmen to get the airship out of Regigigas' firing range. J fires her bracelet at Regigigas to turn it to stone, but Regirock jumps in front of the blast to protect it and is turned to stone instead. J, frustrated, tries again, and again; the blasts are taken by Registeel and Regice instead. J fires the bracelet again now that there is nothing between her and Regigigas, but Brandon, telling Brock to take control of the airship, jumps out and in front of the beam and is petrified instead. Regigigas catches him before he can hit the ground. Before J can fire again, Pikachu and Piplup use Thunderbolt and Bubble Beam respectively. Salamence unleashes Dragon Pulse at the airship, but Regigigas, breaking free of the gum, deflects the attack back at Salamence, breaking J's bracelet. J prepares to attack with another Dragon Pulse, but is interrupted by her henchmen who say that her client canceled the deal, apparently after being frightened by the destruction. She and her henchmen leave the area immediately. Maria apologizes to Regigigas for letting them awaken it, and asks it to save Brandon and the titans. It agrees, using its powers to unfreeze them before returning to the form of an orb.
The gang returns to the ruins of the Snowpoint Temple as the sun is setting. Brandon promises to rebuild the temple and have Regirock, Regice, and Registeel protect Regigigas so it will never be awakened again, and Maria agrees to help him.