Here's one of the final battles!
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The First Cross:
The Crystalline Genesis

(C r u c e -- W a x - W a n)
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-Source of Crystals.-

Cruce: [He nervously begins casting a spell, watching Mewtwo raise another arm.]
Mewtwo: Hm. [He grasps control of Cruce's body, interrupting his casting. He uses telekinesis to throw Cruce against the ice roughly. He holds Cruce against the ice, the Time Gear about to fire another blast of dark energy.]
Wax-Wan: Not so fast! [He closes his eyes, picturing in his head another place... He then teleports to that place, which happens to be in front of Cruce. He conjures a spherical shield of glittering green aura to take the blast. The shield consumes this energy, converting it to Wax-Wan's aura. He instantly returns fire at Mewtwo, then vanishes with Cruce. He and Cruce are returned to Wax-Wan's previous position behind Mewtwo. The corrupted Time Gear moves in front of Mewtwo, creating a red force-field to take the counterblast. Expecting this move, Mewtwo turns half-way, an arm thrust forward to fire bolts of dark purple psychic energy -- his specialty -- at the two.]
Cruce: [He thinks quickly enough to evade this move, however is still struck with the majority of the psychic bolts. He is thrown to the ground, his body glowing with Mewtwo's psychic power.] Aahhh...
Wax-Wan: [He takes a few bolts, but they deal minimal damage.] That Time Gear will be saved! Pity for the demon of Darkness to use such a cherished relic to do his bidding!
Mewtwo: Perhaps you will come to respect my decision once you are a part of it. [Now facing the two, the red force-field remains around Mewtwo but not around the Time Gear. He starts charging up a sphere of electric-psychic-temporal plasma.]
Cruce: ...P-pain... Hurt... [He stands, shaking it off.] He's tough.
Wax-Wan: Cruce! The Time Gear is protecting Mewtwo! We have to eliminate his hold over it without destroying it!
Cruce: Looks like he's giving us the time for that!
Wax-Wan: Yes, quickly! Try to seize the Time Gear if you can! I will ensure your safety!
Cruce: (Don't destroy it, huh...?) I've got an idea! [He begins casting an ice spell similar to the one used to deal with the Nightmare Bear. Before Mewtwo can finish charging, he casts this spell around the Time Gear, encasing it in a block of green ice. It falls to the ground. Mewtwo releases his move on Cruce just as his shield drops.]
Cruce: Ahhh!!
Wax-Wan: I got'cha. [Again, he warps to Cruce, then, as if time has completely slowed down to him, warps back to his spot. Cruce is safe near him. He rushes to the frozen Time Gear, pressing both hands against it and letting his energy flow through the ice and to the Time Gear...]
Mewtwo: Clever attempt. [The Time Gear bursts from the ice in a fiery black rupture, returning to Mewtwo and blowing Wax-Wan back. It no longer charges up powerful blasts rather than firing mini blasts much more frequently. These blasts start for Wax-Wan, but he recovers quickly enough to block these blasts with his shield. At the same time, Mewtwo himself is focusing on Cruce. He performs a move very unconventional for his type. His bright eyes gleam purple, capturing Cruce in psychic telekinesis.]
Cruce: [In midair.] Cr-crap... Let go!
Mewtwo: Very well. [His eyes gleam purple again. The air rips around Cruce in various locations. From these rips, wisps of purple plasma slice through Cruce's body in rapid succession of one another before letting up. He drops to the ice.]
Cruce: Ahh!! [Thump!] Agh--! ...Oogh... (He's... ripping me up...)
Wax-Wan: [Again, he teleports. This time, he moves to Cruce's aid and conjures a dome-shaped shield around he and the other. He crouches to Cruce and places a hand on his back, his own aura flowing into Cruce's body.] He is a worthy adversary...
Cruce: [Closes his eyes.] ...Y-yeah... Thanks... Wax-Wan... I have to be stronger than this.
Wax-Wan: We both have to fight. Side by side. I refuse to let Mewtwo do any further harm to you.
Cruce: [He stands.] Ahh... Likewise... Hm? [Looks around.] Where'd he--!!
[Mewtwo, having been rooted to the ceiling with the Time Gear facing the two and charging, releases his own plasma energy with the Time Gear's at the same time, shattering the Phaze's shield and blowing the two apart.]
Wax-Wan: Ahh--Oof! [Hits the wall.] Ah...
Cruce: [He recovers in midair, feeling much better from Wax-Wan's spell.] Dammit, Mewtwo!! [He begins casting another ice spell as Mewtwo lowers himself back to the ground, the Time Gear hovering ahead and dropping energy "bombs" on the ice below. Cruce, again, freezes the Time Gear. It falls.]
Mewtwo: Persistent pest! [He reaches for the Time Gear, but is thrown back by a sudden air burst from Wax-Wan's teleportation energy. The Phaze warps directly on the chunk of green ice, knocking Mewtwo away from it just in time.]
Wax-Wan: Good work, Cruce! [He hops off, repeating his process from before.]
Cruce: [He starts casting another spell directed at Mewtwo. He casts. Ice jets up from underneath Mewtwo, catching him off guard.]
Mewtwo: [He is thrown into the air.] Gah!! [He warps, appearing in midair at another section of the room. Black spheres materialize at his fists. He raises his arms into the air. Nightmares now start to appear throughout the room. The Nightmares are strictly imps, though they instantly move to the offensive.]
Cruce: You're kidding. Urmph--[He is hit with a swipe from a Nightmare, but returns the favor with a razor leaf to the face. He begins focusing on these Nightmares as the Time Gear again erupts from the ice, knocking Wax-Wan back.]
Wax-Wan: Ah! Hm! That is hard to predict! The Time Gear's beginning to return to its natural state! Just a little more! [He starts battling with a light green fire, controlled with his own psychic energy. The fire spins around him in the form of an asterisk. He flies through the Nightmares, eliminating them easily.]
Mewtwo: This annoyance can no longer be tolerated. The time to break is now. [Dark energy now surrounds the Time Gear as Mewtwo continues to command it with telekinesis. A red force-field once again defends him, though he retains his ability to fire psychic bolts at the two through this force-field.]
Cruce: [He begins flying throughout the room as the Time Gear spins like a blade around the chamber at high speeds, threatening anything in its path. It seems to be following Cruce while Mewtwo fires his bolts at Wax-Wan.]
Wax-Wan: [Defending himself with his own shield. Though his psychic energy has been weakened from his previous encounter with Mewtwo.] There has to be a way to deal with that Time Gear!
Cruce: This is scary! [He flies faster, not daring to look behind him. He can hear the menacing whirring of the Time Gear as if it were coming closer. Then, an idea.] Oh! [He notices where Mewtwo is floating. Carefully avoiding his blasts the saw-like gear follows Cruce's path until he reaches Mewtwo. Cruce swiftly flies under Mewtwo, then back up. The gear does not follow this. Instead it cuts straight through its own dark energy, disrupting Mewtwo and the force-field. It falls to the ground.]
Wax-Wan: [Rushes to the Time Gear.] Without even having to freeze it!
Mewtwo: [Still hovering, he tries to catch his breath.] ...
Cruce: [He readies an energy ball directed at Mewtwo.]
Mewtwo: [Suddenly looks up, his eyes gleaming red. He is now holding Cruce in place.] ...I... will end everything that is you... [Mewtwo again charges up a ball of psychic plasma while holding Cruce.]
Cruce: (!! Can't move! What'd he do to me?!) [He watches, not even capable of speaking. Wax-Wan cannot hear him due to his work with the Time Gear.]
Mewtwo: [The sphere grows larger.] ...You are... over...
Pachi: [Watching from behind the dark field, he cries out.] N-no!!
Cruce: (Pachi... Don't... don't do anything reckless... I don't know... you don't know if I'm gonna die... Wax-Wan said he'd protect me.)
[The Time Gear begins to return to its normal color, albeit very slowly.]
Mewtwo: [The plasma sphere is at its peak.] Now... Now it ends.
Cruce: (It... ends...?)
Grovyle: This is bad!
Riolu: Wax-Wan! Cruce is in danger!
Pachi: [Again, he cries out.] No no noooo!!! Cruuuce!! [As Mewtwo fires the blast, e closes his eyes, his body sparks, and, like a lightning bolt, he charges forth. His time break ability has become so potent that he is able to dash through the split split second flickering of the dark field. He leaps in the way of the blast...]
[Cruce falls to the ground on his feet. Pachi on his side, unconscious. His body has been temporarily blackened by the ferocious power behind the burst. The bleakness seems to leave Pachi's body like mist, slowly revealing his injured self.]
Wax-Wan: [Turns to face the scene and gasps.] Wh-what?! [The Time Gear has been fully restored to its true state.] Pachi...?!
Cruce: ?! H-how--?! [He runs to Pachi, looking down at him, speechless.] ...Pa-Pach...Pachi, how did... [He realizes that Pachi could possibly be gone by now.]
Mewtwo: ...[Weakened from the burst.] ...Heh...Heheheheh... Hehehehahahahaha!! Such a beautiful sacrifice!! Twas the fate of a powerful Pokémon to sacrifice himself for a hotheaded human! Ahahahahaha! ...And so it ends...
Cruce: [With his head lowered...] ...
Wax-Wan: Cruce... [He holds the Time Gear.]
Cruce: [He remains silent...]
Wax-Wan: ...Mewtwo... you...
Mewtwo: Heheheheh...[Watching Cruce with his palms glowing with purple psychic aura again.] Come at me, boy! Face me with that anger! [From a strange emotional manifestation, his voice begins to distort to sound like two.] Show Darkness the fury of vindictive Light! Gaze into the eyes of Death and scream! Scream!! [His black essence rises like fire above him with another pitch black figure manifesting, the eyes of hell in this mist.]
Cruce: ...Wax-Wan... guard yourself, you and Pachi... do everything you can to defend he and yourself...
[Wax-Wan warps to Pachi with the Time Gear and then warps back to the spot he had been standing with Pachi. He conjures up a field of his own energy as he realizes he is at a fair distance from them. Next, he commands the Time Gear to summon a secondary shield. Immediately, he begins working on Pachi.]
Cruce: ...(One more time...) ... ...[His body can be seen releasing subtle waves of pressure. At the same time, the room seems to warp and shimmer. The blackness surrounding Mewtwo begins to sink into Cruce's fur. His red scarf darkens.]
Mewtwo: [He notices his manifested aura is beginning to vanish completely into Cruce.] Wh-what?! What is this?!
Cruce: ...This... is goodbye. [He raises his head, now glaring at Mewtwo with a sinister expression, the essence of Darkness swirling around him violently.]
Riolu: [Watching with anticipation and fear.] Grovyle, what is he doing?!
Grovyle: [He steps back.] We have to get out of here! He could bring this entire place down!
Riolu: [He looks back to Grovyle, worried.] What is Cruce up to...?
Grovyle: Seed Flare... I... I have no knowledge of how he is able to use Seed Flare freely; such a move absorbs pollution and releases it as energy.
Riolu: There was no pollution or poison when we were fighting the Nightmares! He used it then?
Grovyle: Yes... it is mind boggling... this boy is capable of very dangerous feats. He... is absorbing Darkness as pollution.
Mewtwo: [He can feel his power slipping away into Cruce.] Agghh!!
Cruce: [At once, all of the Darkness lurches into Cruce's body. He lowers his head again, stressing heavily to let go of this as energy.] Hrrrrr... [Lifts his head and screams.] Aaaaahhhhh!!! [The scarf becomes as bright as the sun. An explosion follows...]
[In the brightness of this explosion, Wax-Wan walks through the scene as if time were frozen...]
Wax-Wan: [He is carrying both Pachi and the Time Gear with his psychic abilities.] ...Your power... what is the extent of your true power...?
"I know this is not it."
Wax-Wan: [Having been restored to full energy due to the Time Gear's recovery, he finds Cruce, then Grovyle, then Riolu. In the folds of time, they are gone...]
"Thank you... for helping me restore my power."
"I might... have been lost... without you."
"...Can you do the same..."
"For Supernova...?"
[The explosion continue with Mewtwo still inside... The cave begins to collapse.]
--E n d i n g--