After returning Goodra to its home, our heroes are suddenly confronted by a giant creeping vine—just like the ones Team Flare unleashed on Lumiose City! The scientist Xerosic is trying to continue Lysandre’s work, and he even turns a mind-control beam on Clemont! But Clemont is too clever for that—a secret invention rescues him, and Xerosic is arrested.
When another vine attacks our heroes, Squishy and Zygarde come to the rescue…with a difficult request. Ash’s Greninja is able to sense the energy feeding the vines, and Squishy needs its help to stop them. With Ash’s encouragement, Greninja agrees, and joins Squishy to help protect the Kalos region!
Ash and his friends have traveled to the wetlands in order to return Goodra home. Ash thanks Goodra for battling alongside him again and promises that this isn't the last time they'll see each other. A tearful Dedenne jumps up for a hug. Everyone says their final goodbyes before heading back to Lumiose City. On the way, Serena discovers that Lumiose Airport is running again, meaning that she can head to Hoenn while Ash can return home to Kanto. Clemont notes that their journey is nearly over, which makes everyone feel sad. As they continue on their way, Ash senses something heading their way. Greninja, sensing it too, appears out of its Poké Ball. Ash wonders what is going on as roots come up from out of the ground. Clemont realizes this is the same as what happened in Lumiose City. Clemont believes that this must be the work of Team Flare, but Bonnie points out that Squishy got rid of them. Ash decides they need to get rid of the roots right away, and Greninja transforms into Ash-Greninja. They both see the power inside the roots; Ash has Greninja use Water Shuriken, which defeats the root as a Zygarde Cell watches from a tree. A deep rumbling begins to occur as a large truck nearly runs them over. The Cell watching them is suddenly picked up and dragged towards the truck because of Xerosic and his Malamar. Clemont informs the others he was Team Flare's Scientist. Xerosic isn't happy at being defeated and has come back, planning to create Team Neo Flare. Bonnie tells him to give back Squishy's friend but he says he won't do it as he plans to obtain Zygarde Complete Forme and make Lysandre's dream come true. Ash has Greninja use Water Shuriken to smash the device but Malamar stops it with Signal Beam before lifting Clemont off his feet. The truck departs, taking Clemont captive, as Greninja chases after it.
Inside the truck, Xerosic informs Clemont that his scientific knowledge will be useful, but Clemont says he'll never help him. Xerosic is unfazed by this as he has other plans, namely to use mind control on Clemont like he did with the Zygarde and make him an advanced human. Xerosic releases Clemont from his restraints and prepares to use the beam but Clemont asks for a chance to clean his glasses first. Xerosic is surprised at this request but allows him to do it before firing the beam and causing him to scream. Nearby, Team Rocket are going over the footage they shot during the Team Flare incident and editing it to make them look good. They start arguing about where parts of the footage should go, trying to make each of them more prominent, when another root pops up and attacks. Suddenly, Squishy and Z2 come over in their 10% Forme to destroy the root. Wobbuffet recorded the whole scene and James decides to edit it into the video. The truck screeches to a halt where another Cell is. As Xerosic and Malamar go to look, Greninja comes out of hiding and Ash can see that Greninja has found them. However, he doesn't know where Clemont is, so he has Greninja try and sneak inside. Spotting a Cell, Xerosic has Malamar use Psychic which collects the Cell and puts it into the truck. Greninja is near the truck when it steps on a branch alerting Xerosic, who spots Greninja and orders Malamar to use Signal Beam. Greninja dodges and attacks with Water Shuriken as everyone arrives on scene, demanding Xerosic to release the captives. Xerosic decides to retreat for now and orders Malamar to use Psycho Cut, which briefly stops Greninja. Greninja follows after the truck and jumps in front of it, appearing to get run over but Ash realizes Greninja is hanging on under the truck. They chase after the truck, but it flies off and becomes invisible. Xerosic believes he has gotten away and that the machine should be ready. However, thanks to Greninja, Ash knows where they are.
Xerosic returns to Clemont who says that he feels great, and being called the leader of Team Neo Flare makes Xerosic feel satisfied. Ash, Bonnie, and Serena reach a tall rock and Ash tries to figure out where Greninja is. Greninja sees Ash, causing Ash to realize where Greninja is, and decides to jump, much to Bonnie and Serena's surprise, who become worried. As Ash prepares to jump, Serena says she'll go too, as does Bonnie. They all jump together but miss, but Greninja catches them with his tongue and brings them onto the ring. Inside, they come across Clemont, but are stopped by Xerosic who tells them Clemont is being mind-controlled. Clemont confirms this and is ordered to capture them. Ash says Clemont would never give in to mind control, and Clemont reveals having never been under Xerosic's control because he placed a device called the Jamming Unit 1 in his glasses to prevent it from working. Xerosic orders Crobat to use Air Slash but Clemont brings out Chespin to counter with Pin Missile. The attacks collide as Ash has Greninja team up with Chespin. Xerosic orders Malamar to use Signal Beam and Wing Attack but with Vine Whip, Chespin is able to dodge and hits Crobat with Tackle. Xerosic becomes angry about this and calls for another Air Slash but Greninja strikes back with Water Shuriken and knocks out Crobat. Xerosic recalls Crobat as he states he will be able to recreate the world. He goes to jump out and recalls Malamar. Clemont uses his Aipom Arm to catch Xerosic.
On the ground, Officer Jenny has Xerosic in handcuffs and before being lead away asks Clemont why he is so strong. Clemont replies it was thanks to spending time with Ash, Bonnie, and Serena, which surprises Xerosic as he is taken away by Officer Jenny. Serena is glad it is over as Bonnie addresses the Cell asking if it knows Squishy. Just then another root springs up from the ground, but it is destroyed by Squishy, who has just arrived. Bonnie is delighted to see Squishy again and hugs it. After being reunited, Squishy asks Greninja to follow it, which Greninja does along with the others. They come across Z2, who speaks telepathically to Greninja and explains that although Team Flare was defeated, Kalos is still bearing the scars of the attack, which manifests as the underground roots. It is hard for them to find their exact locations but Greninja is able to locate them easily. Ash tells Greninja what happened before can never happen again, and reminds Greninja about what Professor Sycamore said about them meeting not being a coincidence and their powering up not being an accident, and that this was meant to happen. Ash allows Greninja to leave so that Greninja can track down all the negative energy. They shake hands and hug as the others look on. Greninja goes to leave as Squishy says that Greninja will be under its care and tells Bonnie while they may not see each other for a while it will always be with her. Bonnie understands, and promises to meet up when she becomes a trainer so the two can go on another adventure. Squishy agrees, telling her it's a promise. Everyone says goodbye as they set off on their separate ways.