Outside the Nacrene Museum, Black stands before the legendary Tornadus, Thundurus and Landorus, and demands them to let go of the Gymleaders. Nite, who has just evolved into an Emboar, struggles to hold its trainer back, as it knows that he will get hurt if he continues to act recklessly.

The Shadow Triad mock that a wimpy trainer isn't worth their time, and get Landorus to smack him back with its powerful tail, which send the boy and his Emboar crashing hard into the wall. The three masked men watch as the Six Gymleaders are trapped and rendered helpless within the combined tornado created by the genies, and make fun of how arrogant they were when they had the upperhand.

Just then, three female Plasma Grunts come out from the museum to report to the triad, and apologize that they have not been able to locate the Dark Stone even after turning everything upside down. The Shadow Triad are surprised to hear that, and turn their attention to Hawes, whom they know is the assistant director of the Nacrene Museum. They get Basculin and Lilligant to close in on the man, and demand to know if it was just a hoax that the Dark Stone is being kept at the museum. Hawes trembles from fear at Basculin's intimidation, and is so frightened that he actually couldn't say a word. The Panpour-masked man believes that the artifact must be kept at some secret chamber, and his suspicion is confirmed by Lenora, who is still tumbling within the tornado.

The Nacrene Gymleader states that the Dark Stone is currently held at her underground chamber which also stores all her special and important bones and fossils, but unfortunately, the only key to that chamber has just been bent out of shaped from the combined attacks of Tornadus, Thundurus and Landorus. She pulls out a distorted metal key to prove her point, and the Shadow Triad simultaneously gasp in astonishment.

Lenora points towards a metallic door on the ground near the backdoor of the museum, and says it is the entrance to the underground chamber. Yet, without the key, no one will be able to access it because its shelter is made by an extremely tough substance that cannot be broken. The Shadow Triad order Landorus, Thundurus and Tornadus to direct their attacks onto the metal door, but just as Lenora said, the metal wouldn't budge, and is merely scratched by the powerful blasts.

Lenora grins that there should be no doubt to her claim now, and says Team Plasma will never be able to get their hands on the Dark Stone, no matter how many powerful Pokemon they bring to attack the metal door. The Pansear-masked man fumes with rage at her mockery, but the Panpour-masked man stays calm, and is certain that they will figure out a way eventually. He states that victory is destined to be on their side, and believes that it will help if they keep the Gymleaders hostages so as to prevent them from interfering with their work again.

Black struggles to get up from his position, and the Pansage-masked man points out that they have one more troublemaker. However the other two doubt that a wimpy trainer like that could do much, and decide to leave him alone. With that, the Shadow Triad call for a retreat, and order their Grunts to evacuate from the Nacrene Museum. The three masked man hop onto Landorus, Thundurus and Tornadus after throwing Hawes into the tornado, and begin to make their departure. Black cries out for the six Gymleaders, but can do nothing but watch helplessly as they are taken away. Right before the genies' tornado disappear from sight, Black locks eyes with Lenora, who gives him a wink. Then, the tailwind of the tornado whips up a storm of sand and dust to blind Black's vision, and when he opens up his eyes again, everyone is already gone.

The boy wears a look of disbelief on his face, and mutters to himself that they have lost the battle. He wonders what he should do now that everyone else is being taken away, and also feels baffled as to what Lenora's last wink to him meant. It's almost as if the Nacrene Gymleader was counting on him for something, and he suddenly bolts with realization what it is.

At that moment, a silhouette appears in the distance, and soon reveals itself to be Brycen. Black is shocked at his presence, and the Icirrus Gymleader reveals that he has secretly escaped from the tornado when the Shadow Triad were occupied with their conversation with Lenora. Black feels glad that at least one Gymleader is safe, and Brycen wants to know what Black was about to say before he returned.

Black explains that although Lenora said there is no way to access the underground chamber with the only key broken, there is actually one other method. Brycen wonders what it is, and Black grins that it is a method he has personally used once to enter the chamber, since the place is not only for storage but also serves as the Nacrene Gym's arena, where he fought Lenora in a Gym challenge previously. He states that while Lenora probably enters the chamber with her personal key through the metal door, all Gym challengers have to access it via the hidden entrance which can only be found after solving a puzzle at the library's shelves. Brycen is surprised to hear that the Nacrene Gym works that way, and Black is quite certain that this is what Lenora tried to tell him with the wink.

However, on a deeper thought, Black queries if he should go and retrieve the Dark Stone, since the metal door seems to be protecting it well. Brycen believes that they should, and reminds Black that Team Plasma promised to figure out a way eventually. If they somehow manage to break through the metal shelter later, the Dark Stone will be at stake and it is better that they carry it off to safety now.

Black thinks Brycen is right, and the two proceed to access the library inside the museum. The man ask if Black remembers how to solve the puzzle, and Black states that he has a way to remember. He gets Musha to clamp on his head to clear his mind, and struggles hard to recall the solution. Soon, he gets a vivid memory of the sequence of bookshelves and books to find, and quickly puts it into action. As he runs from bookshelf to bookshelf, he starts to realize the reason why an ordinary trainer like him to asked to join the battle, and why the Gymleaders insisted that he remain inside the building. Having beaten the Nacrene Gym, he has experience and knowledge of how to access the underground secret chamber with the puzzle method, and this is something that only ordinary trainers know. He decides that once he finds the Dark Stone, he will protect it in place of the Gymleaders, and take it to somewhere far and safe.

Black soon finds the red button hidden in the last bookshelf, and presses it to open up the secret entrance leading to the chamber. He rushes down the flight of stairs, and immediately sees the Dark Stone sitting on the table. He turns around to grin at Brycen, but in that instant, a silhouette materializes behind the Icirrus Gymleader, and before Black could figure out what is going on, a Eelektross charges towards him and clamps its sucker mouth around his head to shock him with a high-voltage electricity. The attack leaves the boy dazed and paralyzed, and he slips onto the ground and he asks Brycen what is going on. To his shock, Brycen pulls off his mask and wig, and reveals himself to be a Plasma Grunt in disguise. The silhouette who owns the Eelektross steps into the light, and Black is horrified to see that it is Ghetsis. The man grins that he is one of Team Plasma's Seven Sages, and thanks the boy for leading him to the Dark Stone.

The Plasma Grunt picks up the artifact from the table to present it to Ghetsis, and Black struggles to get up, but could hardly move his body. Ghetsis believes that Black should take a well deserved rest, as whatever he does will not change anything anyway. He states that they don't have much time to waste, and says they must bring the Dark Stone to somewhere special where their King will be waiting with joy. With that, the man leaves with the Grunt, and Black slowly slips into unconsciousness.

A while later, Ghetsis arrives at the Dragonspiral Tower on his Hydreigon, and disembarks on its top floor where N is waiting. He greets their King warmly, and hands over the Dark Stone to him. The green-haired young man embrace the ancient artifact, addressing it as Unova's founding dragon of black 'Ideals', and remarks that he has been waiting for it. He urges it to wake from its sleep, and to break out from its sealed state to return to its true form, so that it may accompany him in building an ideal world where all Pokemon can be liberated.

As N speaks of his ideals, black energy starts to pour out from the Dark Stone. Then, in a flash of light, the stone expands fully and becomes the legendary black lightning dragon, Zekrom.

Elsewhere, the Shadow Triad receive a call, and answer to find that it is Ghetsis. The man wants to know where they are now, and the three explain that they are returning to the castle with their seven hostages, including the six Gymleaders and Lenora's husband. However, at that moment, the Pansage-masked man notices something odd, and realizes that the Brycen they have caught is a fake ice figure. Ghetsis asks what is going on, and the triad apologize that one hostage, the Icirrus Gymleader, has escaped. Ghetsis muses that they have chosen the same person to disguise as by chance, but believes that it would not make a difference, since everything is already too late.

Back at the underground chamber of the Nacrene Museum, the real Brycen arrives, and notices the fake mask of him on the floor. He also sees that Black has passed out from some powerful attack, and figures that someone must have disguised as himself and tricked the boy into getting ambushed by another. Unsurprisingly, the Dark Stone is no longer on the table, which means Zekrom might get resurrected after all. Brycen walks over to a computer laptop, and presses a button to make a call.

At the Opelucid City, the city mayor and Gymleader Drayden answers the video call, and hears all about the happenings from Brycen. He wants to know where the other stone is, and the Icirrus Gymleader presses on a switch to open up a hidden space in the wall of Lenora's underground chamber. Inside, a white coloured stone that looks almost identical to the Dark Stone sits, and Brycen tells Drayden that the Light Stone is safe.

Drayden remarks that the enemy apparently wasn't aware that the Light Stone would be kept at the same location, and Brycen says now that the enemy has possession of the Dark Stone, it is very likely that they will recover it into Zekrom, which will lead to major power shift to their situation. He believes that although it wasn't part of the original plan, they might have to consider returning the Light Stone into its true state as well, resurrecting Unova's 'Truth', the white dragon Reshiram.

At that moment, the Light Stone rolls off from the hidden space in the wall, and bounces towards Black as if it has a life on its own. Bryce watches as it stops next to the boy, and Drayden wants to know what is going on. The Icirrus Gymleader ponders for a moment, and thinks Drayden should know better than ask. He hangs up the call, and remarks that something big is about to happen. However, before that, one must get prepared and geared up. With that, he lifts Black onto his shoulder, and starts to walk off, telling the boy to get ready for some tough training…