[Alain is talking to Lysandre atop the Prism Tower]
Lysandre, you said it yourself. You had to be strong to protect the world. Is this what you meant by that?
You speak of the power to protect. Just what do you want to protect in the first place? A tomorrow that is worse than today?
TFTeam Flare Grunt
[on a speaker] All preparations are complete.
[Then, the two men watch as Ash and his Pokémon, who are trapped in some sort of restraining device, are lifted to a higher part of the tower, which surprises Alain. Meanwhile, down on the ground, Blaziken Mask, Serena, Clemont and Bonnie have reached the Prism Tower]
BMBlaziken Mask
First we secure the entrance. Use Flamethrower!
BBlaziken
Blay! [A Dark Pulse attack stops its Flamethrower attack]
BMBlaziken Mask
Blaziken!
[The camera pans up to Bryony and Aliana who are standing on a vine]
AAliana
We can't allow that.
AAliana
Sorry, but there's no way you're gonna pass us.
BBryony
This area is off-limits to outsiders.
[This makes everyone cross. Meanwhile, up on Prism Tower, Ash has began waking up]
Huh? [Discovers that he has been captured] What am I doing like this? [Struggles to break free, but to no avail. He then looks down at his Greninja, who is just waking up] Greninja! [Sees the rest of his team, who have awakened] Pikachu! Are all of you okay?
Hello, Ash. [Ash looks down at him]
Lysandre! Alain, what's going on? Let us go!
Forgive me for your regrettably rough treatment, but we can't release you.
[Ash and Pikachu see Zygarde]
Zygarde! [to Alain] Alain! What's this about?!
[Alain is still silent]
You see, Ash, you may be one of the chosen ones.
ZZygarde (Z2)
[in it's 50% Forme, speaking telepathically] Greninja, I've come to ask a favor of you.
Was that the voice of Zygarde?
ZZygarde (Z2)
The vines that reappeared, the roots have burrowed themselves deep into the ground, and they emerge by absorbing negative energy. What we destroyed was merely on the surface. The scars from the incident that nearly destroyed the world are deep! The two of us are destroying the roots that are scattered throughout Kalos one by one.
SSquishy
[telepathically] However, it's difficult for even me to pinpoint their exact locations, yet, Greninja, it seems that you are somehow able to locate them.
GGreninja
[in its Ash-Greninja form] Ja. [Yes.]
[gasps, then remembers the negative energy from the evil roots] So that was the negative energy...!
ZZygarde (Z2)
I do not know why only you possessed that power, but I am in need of your assistance.
SSquishy
Will you help us with your power?
[Gasps as Ash walks up to Greninja, which is now faced with the decision of its life.]
What'll it be, Greninja...?
[Greninja turns around and closes its eyes in a serious manner.]
[solemnly] I know. What happened before can never happen again.
[Greninja nods to Ash.]
Remember what Professor Sycamore said?
[A flashback of Greninja taking Pikachu's deflected Electro Ball to keep Pikachu healthy as a Froakie plays out, followed by the scene where Ash rushes to Sycamore's lab with it barely conscious in his arms.]
That maybe... it wasn't a coincidence that I met you way back when you were still a Froakie. I think that maybe, he was right. It wasn't a coincidence.
[Flashbacks of Froakie evolving into Frogadier and later defeating Anistar City Gym Leader Olympia play.]
That when you and I power up, it isn't an accident. Maybe your power was always meant for this moment.
[Flashbacks of Frogadier evolving into Greninja, battling Sawyer's Sceptile, and saving a Spewpa in the Winding Woods, followed by it and Ash shaking hands, play.]
Thanks. You always became stronger to help someone else. So now this time, you'll help Kalos and the world!
It's like something's telling you that what you need to do now is find all that negative energy! Don't worry! We'll always be connected, even we're not in the same place!
The truth is, we won't ever really be apart.
This is what you've gotta do!
GGreninja
[nodding its head in understanding, realizing the future of the world of Pokémon lies in its hands] Gren.
[It walks up to Ash and extends its arm out, then Ash and Greninja clasp hands and embrace.]
[emotionally] Oh, Greninja...
GGreninja
[emotionally] Greninja...
[Serena, Clemont and Bonnie watch on distraught as Greninja turns away from Ash and walks towards Squishy and Z2.]
[with tears in his eyes] That's right. This is how it has to be.
GGreninja
Greninja. [It extends its arm to Squishy.]
SSquishy
[telepathically] Thank you.
[to Ash] Ash, Greninja will be in my care.
Yeah! I'm counting on you, Squishy!
[concerned about the future of her and Squishy's friendship] Hey, Squishy...?
SSquishy
We probably won't see each other for a while, Bonnie...
[almost breaks down crying, but is suddenly cheerful through her tears] It's okay! I know that you've got a lot of important work to do! I'll always be cheering you on, you know?
SSquishy
I'll always be with you too, Bonnie.
I'll come and find you when I become a Trainer! We'll be together again, that's a promise!
SSquishy
Yes, that's a promise!
[Dedenne and the rest of Ash's Pokémon express their farewells to Squishy, Z2, and, most importantly, Greninja]
Take care of yourself, Greninja!
You too, Squishy! Take care!!
[Greninja holds Squishy in its hand and looks back as it leaves Ash and his friends]
Greninja and Ash may be parting ways, but this also means the beginning of new encounters! In search of their own new encounters, our heroes will no doubt experience many new and exciting adventures, as the journey continues!
[Dedenne, not wanting to say goodbye to Ash, Serena, and their Pokémon, has run off, sending the gang in a chase around Lumiose Airport. Using Pikachu's electricity, they find it hiding behind a conveyor belt's TV screen.]
[concerned] Pi... Pika-pika!
[startled] Ne... Ne-ne-ne?!
Dedenne! Dedenne, come out! I'm begging you!
[in protest] Ne... Ne! Denne! Dene-nne!
Dedenne, you've just got to come out here! Please?
Denne-denne! [breaks down crying]
I know why... Dedenne doesn't want to say goodbye to everyone.
[Her face sulks before she starts a speech.] What do I do? I need you, Dedenne! I understand what you're feeling! [Dedenne is seen still crying.]
I just know you want to stay together forever because we've all had so much fun together! Well, so do I. I love everyone too! [shots of Clemont, Serena and Ash, who completely understand the meaning behind Bonnie's speech and feel Dedenne's problem, are shown.]
But we all have dreams of our own. Serena, Ash, and everyone wants to try to make their dreams come true! Sure, I'm really sad, but I've got to be strong! [Dedenne starts to wipe off its tears.]
[Bonnie clutches her heart and speaks with determination and sincerity.] When I get old enough, I'll be a Pokémon Trainer! And I'll want you to be my partner!
[Dedenne's voice can quietly be heard as it tries to wipe away its tears.]
I'll become a Performer who's just as good as Serena! I'll earn a Gym Badge from my brother! We'll beat Ash and Pikachu! And then, we'll become number one in Kalos! [Shots of the gang in order of mention are seen, who are humbled by Bonnie's confidence to match what their feats throughout their journey together.]
[Dedenne, still hiding, turns its head towards Bonnie.]
[Bonnie is now cheerful, knowing her resolve when the time comes.] And so, let's dream too! We can say our goodbyes, and still laugh together! What do you say?
Ash, thank you. [holding her hand to her heart, specifically the blue ribbon Ash gifted her] I'm glad I came with you. You're the kind of person I want to be!
[Ash gasps, having been taken aback by this sudden admittance]
[Clemont and Bonnie look at each other and laugh, knowing exactly what she means, and are happy that Ash finally seems to understand to an extent...]
Next time we meet, [winking] you're gonna like the type of person I've grown into!
[smiles and confidently clenches his fist] Awesome!
[laughs, albeit a little nervously] See you...!