Team Plasma is still working on its evil plan: catching Pokémon for use as research subjects with the ultimate goal of world domination. Two henchmen, Schwarz and Weiss, are holding a Braviary captive as they make their way back to headquarters, but they soon encounter a roadblock—set up by N! He uses the distraction to break into their truck and free Braviary, and the two of them escape—but they’ve both been injured by the grunts, and Braviary has a hidden tracking device attached to its neck.
Meanwhile, our heroes are on their way to the White Ruins when they come across the injured pair. They all go to the Pokémon Center, where Nurse Joy bandages Braviary’s injured wing. During a mysterious blackout caused by Team Plasma, N discovers the tracking device and realizes he must get Braviary out of there quickly! He explains his plan to Ash and the others, and they leap into action. Schwarz and Weiss chase after the tracking device’s signal, but they quickly discover it’s just N acting as a decoy to lure them away while Ash, Iris, and Cilan get Braviary to safety!
But Braviary senses that N is in danger, and keeps struggling and calling until our heroes figure out what’s going on. They return to the scene just in time—N is under attack from the henchmen’s Pokémon! Ash knows that N dislikes Pokémon battles, but there seems to be no choice here, and a fierce battle soon ensues: Zangoose and Seviper on the villains’ side against Ash’s Pikachu and Iris’s Excadrill—with a little help from the wild Braviary, who turns the tide in our heroes’ favor. Schwarz and Weiss flee, promising to catch Braviary another day.
It’s finally time for Braviary to return to the wild, and time for our heroes to resume their journey—but this time, N is going with them!
Two Plasma Grunts, Schwarz and Weiss, are driving a truck at night. They encounter a roadblock and momentarily stop; as they move the barricades out of the way, N sneaks behind the truck and places a small device that unlocks the truck's back door. Upon opening the doors, N finds a caged Braviary with an injured wing. N frees Braviary and they attempt to get away. However, the grunts see him and they send out Seviper and Zangoose to stop him with Bite and Scratch, respectively. N manages to block the attacks, saving Braviary, but they fall off the cliff in the process. N and Braviary run away, but Schwarz and Weiss have a tracking device on Braviary's neck that will pinpoint his location.
Meanwhile, Ash, Iris and Cilan are still on their journey to the White Ruins. Ash and Iris are anxious to get some rest and food. Cilan assures them there's a Pokémon Center nearby. Suddenly, N and Braviary run out of the forest in front of them and collapse from their injuries. N tells then that Braviary's wing is injured and the group takes them to the nearby Pokémon Center. Nurse Joy tends to Braviary's injuries and mentions that Braviary will be temporarily unable to fly until they are healed. N thanks her for help and comforts Braviary. Ash scans Braviary with his Pokédex and asks N what happened. N states that Braviary got captured by Team Plasma, in which Ash, Iris and Cilan exclaim that they encountered Team Plasma when they were using EM Waves to control Pokémon. N states that his mission is to liberate all the Pokémon under Team Plasma's control. The group propose to help N, but he tells them that the mission is his alone.
Schwarz and Weiss track Braviary to the Pokémon Center. Ash and his friends are pleased that N deeply cares about Pokémon and that they cannot forgive Team Plasma for capturing Pokémon. Schwarz and Weiss decide to cut the Pokémon Center's power to disarm the security system so they can sneak in and retrieve Braviary. During the blackout, N finally notices Braviary's tracking device. Ash, Iris, and Cilan are curious as to what caused the power outage and Cilan states that the outside lights are still on, so the issue is specific to the Center. N comes in with Braviary to inform them that the power outage was caused by the same Team Plasma members that captured Braviary. Nurse Joy and Audino decide to go check the circuit breakers and Schwarz and Weiss sneak behind her. They enter the room where the Pokémon are resting and use night-vision goggles to find Braviary. They are too late as they see that Braviary's tracking device is moving. They go outside and see N and what appears to see Braviary. They send out Zangoose and Seviper and attack N with Slash and Bite. It is revealed that Braviary wasn't there and that they have been fooled. They turn to N and demand to know where Braviary is, but N runs away, forcing the them to order their Pokémon to chase after him.
Meanwhile, Ash, Iris and Cilan are taking Braviary in the opposite direction. Ash and Cilan recall N telling them that they need to release Braviary somewhere safe. Iris runs ahead and finds the perfect location. However, Braviary refuses to go back as he is worried about N. Ash orders and begs him to stop, mentioning that Team Plasma grunts will only capture him again. Ash realizes that Braviary knows that N is in trouble and Braviary dashes off to find N.
N is still running away from Zangoose and Seviper but they find him and the two grunts catch up. Schwarz orders Seviper to use Screech and Weiss orders Slash on N. N proclaims that he will never give up on his mission to save Pokémon and the two grunts order another round of attacks. However, Braviary gets here just in time to save N, along with Ash, Iris, and Cilan. Ash calls on Pikachu and Iris sends out Excadrill to battle Zangoose and Seviper. Ash apologizes to N that he and Iris are battling but states they have no choice at this point. During the battle, Cilan reminds Ash and Iris to not underestimate their opponents as Seviper and Zangoose are well trained. Excadrill finally beats Seviper with Focus Blast and is recalled because Seviper's Screech has weakened him. Meanwhile, Zangoose and Pikachu collide with two Iron Tail attacks and both Pokémon are struggling to get up. As Zangoose is about to finish Pikachu off with Mega Punch, Ash calls out to Pikachu to get up. Seeing Pikachu is in trouble, Braviary tears off his bandages and intercepts Zangoose with Wing Attack. N watches the battles with awe. Ash then tells Pikachu to finish Zangoose with Thunderbolt. Schwarz and Weiss retreat after their loss and Ash thanks Braviary. Later, Ash, Iris, and Cilan watch on as Braviary is released back to the wild. N tells him that this is where he was meant to be and that he won't need to worry about Team Plasma again.
Upon seeing N's injuries, the group takes him back to the Pokémon Center so Nurse Joy can treat him. N mentions that he will be going a bit past Driftveil City and they invite him to travel with them. N mentions that despite all that happened, he is still against Pokémon battles. However, he confesses that after seeing them battle, it made him experience feelings that he never felt before. So N decides that it will be an honor to travel together with the group for a while.