It is night time at Nacrene City. At the Nacrene Museum, Team Plasma's three masked men, also known as the Shadow Triad, land on the porch of the second floor, and get ready to action. However, a voice comments that the entrance is on the first floor, and on top of that, they are already closed for the day.

The three turn around to see museum's director Lenora and her husband, Hawes, and the dark-skinned woman wonders if they are surprised to be caught. The Panpour-masked man states that they actually anticipated this, and the Pansear-masked one says their companions have had their hands on a dragon skeleton inside before which was absolutely stunning. Lenora laughs that the dragon skeleton he is thinking of is unfortunately an ordinary one, and the Pansage-masked man remarks that they have therefore come for the real thing this time, the founding dragon which their King seeks.

With that, the three men send out a Lilligant, Basculin and Larvesta, who immediately start attacking. Lenora pushes Hawes out of the way, and demands to know if they are from Team Plasma. The three men confirm her suspicion, and suggest her avoid the unnecessary conflict, and hand over the Dark Stone that is Zekrom itself. The Nacrene Gymleader sends out Patrat and Stoutland to fight, and hopes that Clay and the others will arrive soon.

Inside Skyla's cargo plane at the Mistralton airport, Clay is starting to get impatient and grumbles under his breath. Burgh giggles that feeling angry will not help, and Clay hollers that their current plan depends greatly on timing. It is getting close to their departure time, but Skyla is still nowhere to be seen. Elesa believes that she must still be battling Black, and Clay asks Brycen if they should head over to the Gym to get them. However, after remaining silent for a moment, the Icirrus Gymleader opts to wait, which causes Clay to fume that no one is helping out at all.

Meanwhile, at the Mistralton Gym, Black orders another Heat Crash from Nite, and the attack faints Swoobat after slamming it onto the ground. Skyla is shocked that her Pokemon is knocked out, and thanks it as she retrieves it into its Pokeball. She sends out Swanna to fight next, and Black decides to pull off the same strategy by hitting it from a distance with Ember, and then finishing it off with Heat Crash. He orders Nite to fire its flames, but Swanna unleashes a Water Sport, which greatly reduces the power of fire attacks. Black feels troubled that Swanna is not only of the flying type but also has water in its typing, and know that they put Nite at a great disadvantage. Skyla then orders a BubbleBeam, and the supper effective attack quickly faints Nite.

The Mistralton Gymleader recalls that Black is a trainer who does extensive research in preparation for his Gym challenges, and is astonished to see such erratic and spontaneous battle strategies. Black grunts in frustration, and sends out Costa as his second Pokemon. He orders an Ancient Power, but the Tirtouga turns its head around and raises its eyebrows at him. Black hollers that he needs to win this battle to prove his strength, and urges Costa to work with him. The Tirtouga seems to let out a sigh, and unleashes the attack as it is told, which manages to knock out Swanna in one hit.

Black cheers for its good work, and Skyla puts on a frown as she retrieves her fainted Pokemon. She sends out her final member, Unfezant, who whips up powerful gales around itself before charging forward to attack. To Black's shock, Costa makes no attempt to defend itself when Unfezant strikes it with Air Slash, and even acts as if it has gone down, returning to its Pokeball as it falls. Black gasps in surprise that the attack landed and knocked Costa out, and checks on his Pokedex to read that female Unfezant have better flying abilities than their male counterparts.

Skyla notices Black's distraction, and frowns that the match isn't over yet. She wonders if he would like to surrender and get sent back to Nuvema, but Black cries that he is not giving up. The boy sends out his last Pokemon, Tula, and Unfezant immediately starts circling around it. Once the Galvantula gets confused, Unfezant hits it with an Air Slash, and throws it off its feet. Black gasps at the scene, but finds himself at a loss of instructions all of a sudden as his mind gets clogged. He eventually decides that Tula should use its silk, and orders a String Shot.

The Mistralton Gymleader watches as Tula unsuccessfully targets Unfezant with a series of String Shots, and comments that normally, the electrically charged thread would have an overwhelming advantage against her flying types, but the attacks have all failed to hit. Black grunts that Unfezant seems to be moving quicker than he expected, and on retrospect, what happened to Costa was also extremely odd. He rationalizes that if Costa has stayed in its defensive state, Unfezant's Air Slash would not have caused much damage, let only knock it out. He bolts at the possibility that Costa deliberately took the hit, and Skyla remarks that it is exactly what she saw and thought.

She decides to give him a hint, and tells the boy that the same reason caused the impurity in the bell sound he rung. She states that the bell at the Celestial Tower reflects the mind of the ringer, and clearly, Black's mind was not clear and pure when he rung it. Skyla's words hit Black like a radical, and he realizes how uncertain he has felt since Clay told him that the Pokemon League might be cancelled because of Team Plasma, and how he was asked to join the fight against them. He believes that if Skyla saw his uncertainty, his Pokemon would have seen it too. However, he has not addressed the matter to them, and simply wanted to prove his strength, even starting this Gym challenge when his mind was confused and unclear.

Black knows that he must reaffirm his determination, and tells Tula, Nite, Musha and Costa that he refuses to let Team Plasma interfere with the Pokemon League tournament, which is why he has decided to join the fight to bring them down. He hopes that they could work with him like they always have, and give their best in all the upcoming fight. Feeling a renewed sense of clarity, the boy orders another String Shot from Tula, and manages to score a hit on Unfezant this time.

Later, Skyla embarks on her cargo plane, and tells the others that it is time to take off. Clay wants to know where Black is and how their battle went, but the red-haired girl does not give him an answer and simply tells everyone to put on their seat belts for departure. She then starts the engines, and takes off on the runway.

At the Mistralton Gym, Black is still stuck inside a canon, and watches as the plane goes airborne. He wants to know why he is not released, even after he has successfully beaten Skyla at the end with Tula, and in that instant, the cannon starts to move and angle forwards. Black gasps in horror, and as he fears, the canon propels him out and sends him flying out of the Gym. He soars across the sky, wondering where he is heading, and soon lands on top of the Celestial Tower. He holds his back in pain as he gets up, and slowly walks over to the bell. Remembering Skyla's words, he decides to ring it again, and pulls on the rope.

Inside Skyla's plane, everyone hears the chime of the bell, and the Mistralton Gymleader is glad that the sound is no longer impure. She steers the plane over to the Celestial Tower, and sends out Swanna, who flies down to Black and presents him with the Jet Badge. Skyla then speaks through the loudspeakers from her plane, and congratulates Black for beating her, as well as being able to ring a pure bell sound that could sooth the spirits of Pokemon. She invites him to join them on their quest to protect the Dark Stone, and the boy gladly climbs onto Swanna. Getting everyone on board ready, Skyla steers the plane towards Nacrene City as Swanna follows with Black from behind. On the horizon, dawn is starting to break.

Back at Nacrene City, Lenora is starting to tire from having battled the Shadow Triad the entire night. The Pansage-masked man states that they have been waiting for them to lower their guards, but didn't expect them to be so weak nevertheless. The Pansear-masked man says it is time to finish things off, and in that instant, a voice from above calls out that the battle is far from over.

Lenora looks up with a grin, and says they have finally arrived. The Shadow Triad direct their gaze upwards, and are astonished to see five Gymleaders disembark from a cargo plane with their Pokemon. Landing one by one, they join Lenora to take combative stances, and while Brycen chooses to stay silent, everyone else introduces themselves: Burgh the premier insect artist, Elesa the shining beauty, Clay the underground boss, Skyla the highflying girl, and Lenora the archeologist with backbone.

The Shadow Triad gasp in realization that this is part of their scheme, and know that they have been tricked to come at a time when a full fighting force is waiting. The Gymleaders congratulate them for their correct guess, and state that they will not hand over the Dark Stone to Team Plasma. With that, they stand in line, and all send out their Pokemon to attack. Up in the air, Black arrives on Swanna, and exclaims in astonishment that the battle has begun.

Meanwhile, at N's Castle, a monitor connected to hidden cameras displays the situation at the Nacrene Museum to the Seven Sages, who are also surprised by the Gymleaders' unexpected assembly at the site. Ryoku curses their stupidity, and Rood wonders if it will be alright. Giallo reassures everyone that he has foreseen such situations and equipped the trio with adequate battle forces, and is certain that they will succeed in obtaining the Stone. Just then, Ghetsis turns to leave, and the other Sages wonder where he is going. The man explains that he shall make a trip to the battleground, and gets his Hydreigon ready…