The Everlasting Pokémon Journey

...asking your Lilligant what she knows. She tells you that after one disguise too many this particular Jessie accidentally turned herself into a Pokemon. James agrees and says that if that Jessie would talk she would merely say her name. You decide you need to seal the other plot holes and find the other Jessies and possibly other Team Rockets. James says it won't be easy. You and Lilligant decide to start by...
 
...finding the exact location of all the plot holes. So you fly to Pallet Town to see if Oak's Mew could help you out. After giving the Mew a chocolate cupcake, Genesis pokes your forehead with its tail. You now know the locations of every single plot hole and which ones have been opened. How convenient! The closest open plot hole is beneath Red's house. You head to Red's house, but it's surrounded by...
 
... A circle of Froakie and Frogadier, hopping up a down on the lawn, croaking to see the world's greatest Pokemon trainer. A dark-haired boy with a cap, vest and a Pikachu on his shoulder comes out of the house, waves at you and agrees to do whatever he can to help you seal the plot holes. Pikachu scurries over to the family of frog Pokemon to find out what has brought them here.

Red kneels down and strokes the head of a female Greninja. He looks at you and says, "Pikachu tells me that Greninja is looking for her child. It hasn't been home for days. She says she wants a good Pokemon trainer to investigate. I told her you and I would be happy to help. How about we work together to find out what happened to Frogadier and fix these plot holes?"

Feelings of guilt and confusion wash over you as you look at the frog pokemon and trusting young trainer. You decide to...
 
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... you were subdued by the officers -- knocked down and handcuffed into the police van without much question. You told them that it wasn't you that did it, yet they were unconvinced otherwise. The van took off at the speed of light, the next second you were put inside the cell of the detention center due to being charged for murder and destructive behavior. Your Pok?mon and belongings were also confiscated. Inside the iron bars, you let the time flew by...
 
...suggests digging your way out. You do so until you hear a loud 'Pika' you look up and see Red and his Pikachu. He explains that he is protected by plot armour so didn't die. He lets you out of the cell and promises to put in a good word for your cellmate.

Officer Jenny reluctantly gives you your Pokemon back and you and Lilligant hug. She says as part of your release condition you must help her catch a criminal. Red sportingly agrees to help. So both disguised as Officer Jenny you and Red go to catch...
 
...Ghetsis of Team Plasma! He has installed himself as King of Unova. He sits in N's castle with Reshiram, Zekrom and Kyurem in chains, forced to serve him. N is locked in a dungeon awaiting execution. Ghetsis' Hydreigon laid many eggs and the palace is gaurded by hundreds of Hydreigon loyal to Ghetsis and Drapion to kill any courageous fairies. The castle is filled with booby traps as well that can instantly kill you.

You must complete this quest or you will go back to jail for attempted murder. Your choice is...
 
Edit: I completely failed to notice VisionofMilotic's post above. Sorry!

...to do this quest, but also find another criminal to arrest: Dr. Julius Sycamore, Professor Augustine Sycamore's evil brother. Apparently, the Greninja line was going extinct, but because of Julius's efforts, they are no longer in danger of extinction. Officer Jenny says that he must be captured immediately before any more Froakie could be bred and he must pay for this heinous crime. You head to Professor Sycamore's lab to ask him if he has any info on his brother. However, when you arrive, you see numerous unconscious fangirls on the floor. You quickly hurry inside and you see Augustine Sycamore tied to a chair with his mouth covered with Psyduck tape. You then see Julius Sycamore stare at you. He snaps his finger and everyone is teleported to Ghetsis's lair. You are also now surrounded by Greninja and Hydreigon. You kill as many Greninja as possible, but more keep coming. You then have an idea. You...
 
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...realise with so many Greninja and Hydreigon around you need something to counter dark type Pokemon. You and Red send out your Sylveon and combined with your Gardevoir unleash a giant beam of Fairy Pink light to counter the Hydreigon whilst your Lilligant is battling the Greninja hoard using Petal Dance with help from Red's Pikachu's Thunderbolt. All the dark Pokemon are defeated.

Ghethis stands up and applauds your efforts saying you battle well for a pair of Officer Jenny. Julius Sycamore agrees and says even though you defeated the dark mass he will not release his brother. It appears the two are working together so you and Red decide to...
 
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...A tall, blonde man in a white lab coat looking at you through glass. The scientist taking notes says, "The sphere of illusion makes them see their greatest fears. I appreciate you allowing me to use this invention to hypnotize intruders in your palace. It would be a shame if you executed them before obtaining all of this valuable behavioral research."

"Your were halfway useful for a change Coloress," Ghetsis says standing next to Colress behind the glass, toasting with a glass of wine. "You can collect more data about human suffering when they are fed to Reshiram."

Lilligant tries to stop you as you tussle around your padded cell ripping up pokedolls that you thought were real Greninja in your delirium. The hallucination of Sycamore dancing continues as you...
 
...suddenly begin to have a massive headache and begin screaming. It feels like your head is about to be split open. Worried, your Lilligant begins to panic as she sees blood coming out of the sides of your head. She picks up your backpack (which you somehow still have for some reason), hoping to find something to help you with. Your Lilligant then finds your magical ocarina and quickly begins playing the Song of Healing. You suddenly find that you are no longer in pain, and the bleeding has stopped. You begin to thank your Lilligant, when suddenly...
 
...return to her pokeball, fearful of the type matchup between the flower and the fire dragon. Not to mention this was a shiny Reshiram, that was what was off about it, the traces of gold. What else might be different about Ghetsis' newly enslaved Reshiram? The blue-eyed dragon let out a roar, shaking the walls and ceiling. Red stumbles to his feet and throws a pokeball. Aerodactlyl springs forth with a screech. A battered and angry Red orders the prehistoric pokemon to use Stone Edge. Ghetsis directs Reshiram to Reflect and stops rocks with a magical shield of light. Your next move is...
 
...Talk to Red and order him to have his Aerodactlyl use Dragon tail on the Fire dragon. He does as you say and so the badie was forced to switch out. Realising it was gonna be a 2 on 1, he summoned 2 mons: a Milotic and a Magcargo. Aerodactlyl stayed in while the Greninja you met back at Red's house followed you here and decided to fight for you.

You told Greninja to use Surf and it does as you say, leaving the Magcargo with 1HP from Sturdy. Next was the Milotic's turn, and it used Attract on both mons and they became infatuated, resulting in Aerodactlyl being unable to attack. Worse still, Magcargo then used mean look on your team as well so neither of the mons can esacpe now. You decided to...
 
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...tell Greninja to use Aqua Jet on the Magcargo KOing the Fire Slug. Milotic used Hydro Pump on Aerodactyl causing the Fossil Pokemon to crash into the wall behind you KOing it.

Red straightens his hat and sends out his Sceptile to counter the Hoenn serpent. You wonder why Red would send out a Grass Pokemon when
Reshiram was still around. Your questions are somewhat answered when Sceptile Mega evolves and Milotic falls to Giga Drain before anyone can react. Ghetsis sends out Mandibuzz and Reshiram and you notice...
 
... that it appeared that the battle was a decoy to buy some time for their fusion. Surge of blue, heavy wave washed forward through the area, soon followed with a barrage of icicles jutting from below, discharging powerful electricity through the tips of the formed cold obstacles that were menacing and unnerving. The released electricity has paralyzed everyone barring Ghetsis' side and the now fused Black Kyurem. Its roaring echoed, followed up with a focused blizzard that froze Mega Sceptile at absolute zero. Now their eyes were turned against you -- a 3 vs 1 fight, you decide to...
 
...try to escape. However, there is no running from a trainer fight! All you can do now is beg for mercy. You look at the baddies with your puppy eyes and hope for the best. Ghetsis feels moved for a moment, but then...
 
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