In an underground chamber, Clemont slowly regains consciousness, and finds himself restrained against a bed with metallic cuffs around his wrists and ankles. He is soon greeted by Xerosic, the red-hair Team Flare Scientist, who addresses him as Kalos's Master of Inventions. Xerosic, accompanied by his Malamar, informs Clemont that he is currently at Team Flare's Secret HQ, and the Lumiose Gymleader recalls what Y and her friends said about the organization being an evil one.

Xerosic uses a remote control to release the cuffs on Clemont, and the boy quickly leaps to his feet. He gets into a combative stance, and reaches for Heliosk's Pokéball. However, to his astonishment, all his Pokéballs are gone, and in the next instant, Malamar wraps its tendrils around his face and hurls him against the floor, knocking his glasses off and sending them spinning towards the other end of the room. The Lumiose Gymleader winces in agony on the ground, and Xerosic reveals that his party and equipment have all been seized for security purposes. He uses the monitor screen to show him his Heliosk in captivity, and assures him that his Pokémon will be unharmed as long as he follows his orders. Clemont demands to know what he means, and Xerosic shows him the blueprint of a machine, which he needs him to follow and construct. Clemont steals a glance at the drawing, and is taken aback by its incredible design. He wants to know whose work it is, and is shocked when Xerosic claims to be the one who drew it. Clemont barks that Xerosic should be more than capable to construct it himself in that case, and fails to understand why he is needed at all. However, Xerosic thinks he has failed to make himself clear, and gestures towards Heliosk on the monitor screen while coldly stating that Clemont doesn't really have a choice. He shows Clemont all the raw materials he has prepared, and suggests the boy start working right away.

With that, Xerosic leaves the room, and scurries off to his own lab, feeling grateful for the unexpected pair of working hands which would allow him to focus on his other project. He enters his own lab to meet Essentia, the mysterious trainer who ambushed the Tower of Mastery, and wants to know what she thinks of the upgraded Expansion Suit. Essentia thinks it feels smoother and gives her more fluidity in her motions, and Xerosic is glad to hear that. He states that new functions have been added to the suit, and hopes that she will get a chance to test them out along with its heightened physical capabilities.

Down in the underground dungeons, Grace sits inside her cell, and finds it odd that the patrolling guards have yet to show up that day. Since their capture, the red-suited people have patrolled the dungeons at least three times per day, and she begins to wonder what might have caused their unusual absence. Opposite to her cell, a middle-aged couple who owned a bakery in Vaniville thinks it is perhaps Grace's chance to make her sixth attempt in escaping, and Grace is astonished by their suggestion. Soon, the other captured residents also chime in, and the Rhyhorn Racer is surprised that everyone shares the same idea. The residents reveal that they have initially relinquished all hope and thought they would never leave the dungeon. However, when Grace was recaptured after her fifth attempt in escaping, she has told them not to give up and promised that they would all leave the place and return home together one day. The day before, 15 of them have been taken out for uncertain purposes, and neither has returned. No one knows where they have gone and what shall happen next to the rest of them. That said, instead of living in fear and insecurity, they have discussed among themselves and would rather bet on an escape attempt just like Grace.

Grace ponders on the words of everyone, and believes that they are right and they should try to prison-break together this time. The others urge Grace to reveal how she managed to escape in her five previous attempts, and Grace begins to make a hissing sound through her clenched teeth as she looks up towards a vent near the ceiling. Soon, the little door covering the vent opens up, and a key-ring-like Pokémon emerges from it. Everyone gasps in surprise and wonders if it is a Pokémon, but Grace says she doesn't really know what it is. However, it apparently resides in the dungeon, and usually stays in the vent, which is why its presence has not been noticed by the red-suited people. The baker wants to know if it was the one who helped her escape, and Grace grins with a nod. She recalls thinking why it made so much clattering sound when she first saw it, and later discovered that it was due to all the keys it has collected. Just like Dedennes who gather Berries and Burmys who scout for grass, sand and trash to make their coat, the key-ring Pokémon apparently collects all kinds of keys, which made her curious as to whether it would hold the key to her cell. Indeed, it did and that was how she first escaped from the dungeon. Afterwards, the red-suited people kept changing the locks, but each time, the Pokémon would help her find the right key and aid her escape.

An older man in the group recognizes the key-ring Pokémon as Klefki, and says it never lets go of any key it has obtained. Grace believes that it must still possess the first set of keys to the locked doors in that case, and tells it to distribute them to everyone. With that, Klefki begins to hover back and forth between the Vaniville residents, and one by one frees them from their cells.

Meanwhile, on Route 9, also known as the Spiky Mountain Path, X, Trevor, Tierno and Shauna are looking around for Y but to no avail. X notices a broken boulder, and after studying its unusually sharp edge, believes that it has been artificially slashed recently, which suggests that some kind of battle has occurred. Trevor and Tierno bolt at the implication, and Shauna cries that X should stop scaring them. X continues to look around, and soon sees a foamy object on the ground, which he picks up to examine. Just then, Rhyhorn thrashes around again, and Trevor wonders why it has been acting really strange since they entered the route. At that moment, Shauna notices a man walking by on the path below, and Tierno sees that he is a Rhyhorn Racer. The big boy realizes that they are on a training course for Rhyhorn Racing, and Trevor believes that Y must have taken Rhyhorn to this place before, which would explain its behavior.

Suddenly, Shauna lets out a cry, and points towards an unconscious Sky Trainer on the back of Rhyhorn Racer's Rhyhorn. The group immediately rushes down to intercept the man, but quickly discovers that the fainted person is not Y but her senior Yvette whom she has battled. The Rhyhorn Racer feels glad that they are acquainted with the girl, and explains that another female Sky Trainer has placed her in his care. Trevor quickly asks where the other Sky Trainer has gone, but the Rhyhorn Racer replies that he has no idea, only that she seemed to be in a hurry. Shauna sulks at the response and turns to X, who is still studying the foamy object, which he discovers to be a small pebble coated with frubbles. He recalls having read from magazines that it is a trait of Froakie's evolved form, Frogadier, whose bubble-coated rocks are famous for being difficult to detect by the foe during battles. He points out that more of such pebbles have been placed every few meters apart, almost creating some sort of trail, and Shauna wonders if it could be the work of Y's Croaky. X ponders for a moment, and postulates that Y must have encountered and fought the enemy where the boulder was slashed, during which Froakie evolved into a Frogadier. Afterwards, for whatever reason, Y had to move and thus placed Yvette in the Rhyhorn Racer's care. He thinks Y must have considered the possibility that they would come to find her, which is why she has made Croaky leave behind a trail for them to follow.

Hearing X's words, Shauna is shocked that Y actually used her head this time, and Trevor states that they would be able to locate Y if they follow the pebbles. Tierno thinks they have no time to waste, and the group begins to set off. The Rhyhorn Racer quickly stops them and asks what they plan to do with Yvette, but the kids simply request that he take her to a hospital and dash off before the Rhyhorn Racer could respond.

Later, on Route 8, Malva and Celosia venture deep into the woods as the sun slowly sets. Behind them, Croaky stealthily follows their track while keeping itself hidden in the tree branches. Every now and then, it creates a frubble-coated pebble, and drops it silently onto the ground. At some distance apart, Y keeps up with the pebble trail, and is impressed with what Croaky can do. Not only has it managed to stay unnoticed despite being so close to the enemy, but it is also able to use the pebble trick to keep her on track while giving her enough distance for safety. She steals a glance at the path which she has followed so far, and thinks they may help to guide X and the others too should they come to find her. The truth is, after hearing what the enemy has said, she simply couldn't sit back and do nothing. If they are indeed going to get their hands on Xerneas, who has supposedly become a 'Tree', they must be up to something evil, and another tragedy like the Vaniville incident would occur again unless they are stopped.

Soon, Malva and Celosia arrive at their destination, and even from a distance, Y could see the magnificence of the giant 'Tree' which Xerneas has become. Malva informs Celosia that they are now deep in the forest next to the cliffs on Route 8, and Celosia says she shall return to the headquarters and bring along a labor force of 30. Malva states that she shall handle the Shalour people meanwhile, and Celosia wonders if she means the Mega Evolution Successors. Malva recalls that Celosia has fought the Shalour Gymleader Korrina, and the purple-haired Scientist drops her head in shame as she remembers how she was defeated.

Malva explains that Korrina's grandfather, Gurkinn, acts as an elder of Mega Evolution, and all those in Kalos who wish to wield the skill must earn his recognition and inherit an item embedded with the Keystone from him. One of such people is Diantha, the current Pokémon League Champion and also a renowned actress. Previously, she has instructed Xerosic to kidnap Gurkinn in order to help their Boss obtain the power of Mega Evolution. However, Gurkinn and Korrina ended up abandoning the Tower of Mastery and fled. Afterwards, they met up with Diantha, and the three are currently still on the run. Celosia wants to know if Malva plans to target the three, and the pink-haired woman responds with a grin, stating that she already has the perfect plan to trap them. With that, she sends out a Braixen from a Pokéball, and remarks that she couldn't wait for the moment she burns them all to ashes. Celosia then flies off with Aegislash back to their headquarters, and Malva makes her way even deeper into the woods.

Croaky gestures to Y to let her know that the enemy is gone, and Y slowly steps out from her hiding place. Suddenly, she hears familiar voices from behind, and turns around in pleasant surprise to see X, Trevor, Tierno and Shauna. Overjoyed, the Vaniville kids run towards one another, and feel thankful that they have finally reunited.

Back in the underground dungeons at Team Flare's Secret Hideout, Grace thanks Klefki for its help as the Vaniville residents feel grateful that they have finally been freed. Grace warns everyone not to let their guards down yet, and instructs them to carefully follow her lead. However, the main entrance of the dungeon opens up at that moment, and Celosia steps in with an annoyed look. She wants to know who gave them permission to leave, and gestures to Aegislash, who begins to unleash its spectral powers. In the next instant, the shine disappears from the eyes of Grace and all the Vaniville residents as they are turned into puppets under Aegislash's control, and Celosia states that it is time to set out…