Ash, Pikachu, and Dedenne are in a clearing near a river, relaxing after a meal. Bonnie goes to check on Squishy and starts to sing a song to it. Ash, Clemont, and Serena watch as Bonnie sings, and when she is done singing, Serena calls it a very nice song. Bonnie claims she made it up on the spot. The group is unaware that Team Rocket is spying on them from the shadows, where they also put a call through to Team Rocket Headquarters. Matori answers their call. James asks to be put through to the boss, and Giovanni answers. Giovanni asks if something is wrong, and Jessie responds that there is something he needs to know. James mentions there being an evil organization which stands in their way because they also want to conquer the world. Giovanni asks if they have seen this evil organization, and Team Rocket confirms that they have. Giovanni says he had heard rumours about Team Flare and can now confirm that they are real. Team Rocket is surprised to learn Giovanni has heard of Team Flare. Giovanni instructs Team Rocket to remain in Kalos and find out Team Flare's intentions. Before ending the call, Meowth informs Giovanni that Team Flare is also after a new Pokémon as they transmit images of Squishy to Giovanni. James explains that Squishy is able to combine with certain cells and transform freely. Giovanni instructs them to catch it for Team Rocket before Team Flare does. Giovanni ends the call after telling them that he is counting on them, and Jessie notes that so much has happened since they arrived in Kalos. On top of all that, they must now stop Team Flare, and so, they set off in their Meowth balloon.
Back with Ash and his friends, Chespin and Pancham try and get Squishy to play with them. Instead, Squishy heads off to bathe in the sunlight. Pikachu, Dedenne, Chespin, and Pancham head off to play. Through telepathy, Squishy hears Z2's cries and becomes concerned as Z2 finds itself being chased by a Weavile and Druddigon. Squishy tries to make contact with Z2 while Bonnie wades through the water to join Squishy, concerned that something is wrong. Bonnie guesses that it is sad and sings her song again to try and cheer Squishy up as the others look on. Squishy goes to sleep in the sun, hoping that Z2 is safe. Elsewhere, Z2 finds itself cornered by Weavile and Druddigon as Aliana and Mable arrive with several Team Flare Grunts and praise their Pokémon for their work. Z2 starts to disappear, but Mable fires a beam to restrain it and tells Z2 that it is coming with them. Mable reports to Lysandre and Xerosic that the beam has been effective and Z2 can no longer camouflage itself. As Mable goes to retrieve Z2, Z2 jumps to escape. Aliana orders Druddigon to use Slash, which hits Z2 and sends it flying. Mable sends Weavile in to attack as Z2 starts to collect its Cells to transform into Zygarde 10% Forme. Aliana confirms the previous report from Bryony on the subject while Xerosic watches in amazement. Z2 uses Extreme Speed to attack Druddigon and Weavile. Mable orders the Grunts to attack Z2 with their beams, which miss. Aliana orders Druddigon to use Dragon Pulse, which nearly hits Z2. Mable orders Weavile to use Metal Claw, which Z2 dodges before sending Weavile flying back. As Team Flare continues to fire their beams, Z2 strikes back with Dragon Pulse, causing them to flee. Z2 then uses Land's Wrath to send them flying and flees before returning to its Core Forme. Xerosic tells Mable and Aliana that this is their chance to catch Z2 whilst the beam is still in effect.
Nearby, Team Rocket regroup, having not found a single sign of Team Flare. Spotting Z2 as it collapses, Team Rocket mistake it for Squishy, but James notices that its markings are different, so it must be a different Squishy. As Z2 starts to back away, Team Rocket goes to catch it, only to be frozen by an Ice Beam from Weavile as Team Flare arrives. Team Rocket break free from the ice as Meowth demands to know what that was for. Mable asks who they are, which causes Team Rocket to recite their motto. Mable sarcastically thanks them as Aliana deduces that these are the people that Bryony reported on previously. Mable fires another beam at Z2, and Team Rocket get in the way of the beam as James sends out Inkay to destroy the beam with Psybeam, causing Aliana to send Druddigon out. Mable tells Weavile to use Metal Claw as Jessie sends out Gourgeist to attack with Seed Bomb, which creates a lot of smoke that blocks Team Flare's view. Once the smoke clears, Team Rocket has already escaped with Z2. Mable instructs the Grunts to go and find them, then reports back to Lysandre and Xerosic on what has happened. Xerosic isn't pleased, as Lysandre asks if there is anyone nearby to help them out. Some distance away, Team Rocket has collapsed after running away from Team Flare and getting cramps. As Z2 struggles to free itself, James thinks it has cramps as well. Jessie remembers that Squishy likes to lounge around in the sun, and James sees a place up high where Z2 can get some sunlight. He climbs up to it whilst holding onto Z2, then places Z2 there, where it starts to absorb the sunlight. Upon seeing Z2 glow green with health, Team Rocket decides to report their success to Giovanni, only for their communicator to be hit with Ice Beam as Aliana, Mable, and the Grunts arrive with their Pokémon. Team Rocket state they will deal with them once they get Z2 to headquarters, but Weavile goes to attack with Metal Claw, which causes Team Rocket to go flying as Team Flare demand they hand over Z2. James keeps a close grip on Z2 as Aliana orders Druddigon to use Dragon Pulse, but Wobbuffet takes the hit and uses Mirror Coat to deflect the attack. Team Flare keeps up the attack, with Mable ordering Weavile to use Icy Wind, which sends Team Rocket flying and causes James to lose his grip on Z2. Z2 is then confronted by Sneasel, Skorupi, and Poochyena.
As Team Flare goes to retrieve Z2, Team Rocket attempts to stop them by having Gourgeist use Dark Pulse, which Weavile counters with Metal Claw. The attack cuts through Dark Pulse and strikes Gourgeist. James orders Inkay to use Psybeam, which is countered by Druddigon's Slash. Psybeam strikes Weavile as Druddigon hits Inkay with Slash. Jessie orders Gourgeist to use Leech Seed, which hits Druddigon and starts to drain its energy, but Weavile cuts through the attack with Metal Claw as the Grunts order their Pokémon to attack. Gourgeist and Inkay are hit by Ice Beam and Cross Poison, then are recalled into their Poké Balls as Meowth notes how strong Team Flare is. Z2 finds itself confronted by Weavile and Druddigon as a Grunt prepares to use the laser on it once more, but before they can attack, the ground starts to shake. Z2 starts to gather Cells so it can transform into Zygarde 50% Forme as Team Flare, Team Rocket, Xerosic, and Lysandre look on. Z2 roars loudly. Meanwhile, back with Ash and his friends, Squishy hears the roar and becomes concerned. Team Rocket and Team Flare become nervous over how big Z2 now is before they are all sent flying by a Dragon Pulse. Aliana and Mable declare that this won't end the same way it did back in Terminus Cave as James struggles to make sense of what is going on. Druddigon and Weavile confront Z2 once more, and Z2 prepares to hit them with Dragon Pulse, only to be stopped by a Flamethrower as Alain arrives with Charizard. Alain confirms that Z2 is their target as Aliana and Mable wonder who he is. Alain tells them that he'll bide them some time and orders Charizard to use Dragon Claw as Team Rocket recognizes Alain from before. Charizard hits Z2 with Dragon Claw as Alain decides to Mega Evolve Charizard. Mable orders the Grunts to hit Z2 with their lasers, but Team Rocket, not giving up just yet, vow to stop them. Z2 uses Extreme Speed, which Alain's Charizard blocks, but is overpowered by Z2 before hitting Z2 with another Dragon Claw. Z2 powers up Land's Wrath, which hits Charizard, causing Alain to realize defeating Z2 won't be as easy as he'd hoped. Aliana, Mable, and the Grunts use their lasers at full power to subdue Z2, which starts to wear Z2 down. Z2 begins to transform back into its core form as a result. Mable goes to catch Z2, but is stopped when Team Rocket jumps onto them, saying that Z2 belongs to them. However, Team Rocket is sent blasting off by Druddigon and Weavile. Mable finally captures Z2, which pleases Xerosic and Lysandre.
Alain thanks Charizard for its help as Mable and Aliana speak to him. They thank him for his help, but ask why he answers to Lysandre alone, to which Alain replies that Lysandre gave him a direct order to capture Z2. Later, hanging from a tree branch, Team Rocket report back to Giovanni, who learns that they encountered Team Flare. Team Rocket also inform hims that the new species can transform into a more powerful Pokémon, which will be a great asset to Team Rocket. Giovanni tells them to keep it up before ending the call, and Team Rocket notes that they are going to be busy, especially with Alain and his Charizard, just as the tree branch they were sitting on gives way.
Meanwhile, Squishy is trying to contact Z2 and becomes concerned when it receives no response. Ash tells Bonnie that it is time to go, but Bonnie tells them that something is wrong with Squishy and thinks that it is worried about something. Ash suggests holding Squishy because it enjoys being held, then Bonnie promises to be with Squishy and that everything will be alright.