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The game starts with Jenny and Marble being debriefed by their new Captain, Captain James Avery. Their new mission is to find the person who murdered the city's mayor April Church. The girls have to interview witnesses, collect evidence and get lab testing done with an expert brought in from the Orange Archipelago Lostelle.
They find that it was a pokemon who killed Mayor Church, however the structure of the pokemon is strange as it says that the pokemon is made of crystal. Further testing shows that it is a crystal Steelix. The SCPD releases all the information known on the Crystal Steelix to the public and tell them to be on alert for any crystalised Pokemon. Meanwhile a friend of the girls is running for Mayor, Sabrina the former Gym Leader is running for Mayor against a man named Winston.
Reggie says that he has seen a Shinx wearing a crystal necklace come into the salon, he tells Jenny that the owner seemed very hostile and angry, the Pokemon was scared of him but Reggie couldn't do anything. He tells the girls that he has an appointment for 2:30 today, quickly the girls set up a sting operation.
When the man comes in to collect his Shinx Jenny and Marble watch him closely. Marble is undercover as a customer while Jenny goes undercover as a hairdresser. When the man starts to act hostile the girls break out their badges yelling SCPD FREEZE! The man runs away quickly.
Jenny and Marble chase him around the streets until he is finally caught and he calls himself Flint, the greatest trainer in the world, he sends out his Graveller to attack and then his Golem. When he is defeated he pulls out a whistle which he blows and a crystal steelix erupts from the ground and takes him away.
The girls head back to the beauty salon with Reggie, he tells them that the poor Shinx has no home. Marble cuddles up with Shinx and becomes very affectionate with it, nicknaming it Shinxo and Reggie lets her keep it.
They head back for another debriefing where they are scolded for letting him get away, however they put together a composite of the man and find a match in the system, he is known associates with Eustace and Giovanni. He is a renound hitman across the globe stationed in the Orange Archipelago, his known base of operations in Kanto is in Vermillion City. They tip off the VCPD and Jenny and Marble are sent over.
When they arrive in Vermillion they see that the city is overrun with a punk gang of teenagers who have some how got a bunch of powerful pokemon from the Safari Zone including a herd of Tauros and Miltank. The girls have to round up all of the pokemon and take care of the punk kids before they can go to their debriefing in Vermillion.
In Vermillion they find that the top detectives from around the country have been brought in as well as top rangers from the Orange Archipelago. Detectives Ryan and Bradley from Fuchsia City, Detectives Lisa and Jess from Celdaon City, Detectives Lola and Timothy from Pewter City, Detectives Andrew and Michael from Cerulean City, Detectives Liam and Leslie from Vermillion City and Rangers Amber and Ashley from the Orange Archipaelago. They have been gathered to share intelligence about Flint and his known affiliate Eustace in attempt of catching them.
The girls head off to the Pokemon Centre first as they visit their friend Joy and they find out if she has seen Flint. When arriving there Joy says that she has indeed seen a man matching Flint's description saying that he was a lovely and polite man that came in earlier and dropped off his Graveller and Golem.
Jenny and Marble call it into the station as they wait inside the Pokemon Centre while detectives Liam and Leslie wait outside under cover, Detectives Lola and Timothy wait up on the roof of a neighbouring building with their bird pokemon and Detectives Lisa, Jess, Andrew and Michael pose as a group of friends at one entrance of town and Rangers Amber and Ashley and Detectives Ryan and Bradle pose as friends at the other exit of town.
When Flint comes in to pick up his pokemon he recognises Jenny and Marble, he turns to leave only Liam and Leslie come in and block the doorway so he can't escape. He calls upon his crystal Steelix again, it burts up through the ground causing the building to become wobbly. Jenny shouts and tells everybody to leave the building while she runs up stairs to save the rest of the people before the building collapses.
When she escapes from the building she sees that the other detectives are allready battling against the Crystal Steelix, Flint has run away. As Jenny joins the fight so does her long time companion Squirtle. Steelix takes out the other detectives with one strong swing of it's tail. It focuses it's self on Jenny. After it's defeated the thing is placed under a very strong net.
The other detectives including Marble are in the hospital which is also the temporary location of the Pokemon Centre while it's being rebuilt. The Crystal Steelix has been moved to Pallet town where Professor Garry Oak and Professor Lostelle Gum are working on analysing the great beast. Temporarily Jenny is assigned a new partner. Detective Timothy from Pewtwer City, his partner Lola had flown down to fight the Steelix while he had stayed behind.
The temporary pair are assigned the job of protecting Sabrina as she makes her way to the mayoral debate against Winston. Winston has known gang affiliations and Sabrina has asked for protection from the police so Jenny is sent back to Saffron with her new partner.
They great Sabrina as she gets off the Magnet Train and they must escort her all the way to City Hall, she refuses to travel by limosuine because she wishes to connect with the people. Many gang members do try to attack her only to be stopped by the two detectives, when she reaches City Hall she thanks the two detectives and tells them to watch the debate tonight. Timothy dismisses the comment however Jenny being friends with Sabrina knows of her psychic abilities and makes sure to watch the debate.
The debate begins with a Mr. Mime coming out in front of Sabrina while a Pinser comes out in front of Winston, a tradition that their first pokemon come out in front of them. She steps in front of her podium when a shot aimed at her echoes through the hall, only to be deflected by light sheild. Jenny and Timothy (who she had forced to come to the debate) jump into action and run after the shooter while Sabrina remains perfectly calm.
The two run through the streets of Saffron and find that the scum comes out when the lights are low. Timothy brings out his Swalot and takes to the skies while Jenny continues on foot after the man. They find him and end up at what was long thought to be a notorious gang hideout but could not be proved until now.
The next day Timothy and Jenny tell Cheif Avery of the hideout and they insist that they go in undercover. Jenny under the guise Liv and Timothy under the guise Eli sneak into the club. Their cover story they are a wealthy couple from Pewter City and they need the wealthy tax cuts that Winston is proposing. They want to help in whatever way they can. They infilatrate the club succesfully and take many files.
During the mission as part of their cover Timothy and Jenny kiss, Jenny is all ready dating Reggie. The night after they go home the two kiss again. They seem to have kindled some sort of relationship, Jenny feels bad for cheating on Reggie but she wants Timothy more than she ever did Reggie.
Election Night comes and this is the night that the gang is busted by the cops "Liv and Eli" attend a party thrown by Winston and when they give the signal the police storm the mansion and the gang is busted. Jenny and Timothy race through the mansion to find Winston.
Timothy and Jenny split up he goes down the hall and she goes up where she finds Winston who won't go down without a fight. She defeats and arrests Winston just as it's announced that Sabrina is the new mayor of Saffron City anyway.
Jenny and Timothy return to the station house with Winston in handcuffs. He is arrested and Jenny finds out that her partner Marble has been moved to Saffron Hospital. While Jenny leaves Captain Avery tells Timothy that he can transfer to the SCPD if he wants, otherwise he will need to return to Pewter City in a fortnite when Marble is healed. Timothy says that he will get back to the captain.
A week passes and a new lead finds that Eustace has been sheltering Flint in a small village hidden outside of Saffron. Timothy and Jenny sign themselves up to do the mission, they have been continuing their relationship in secret while Jenny still dated Reggie, it is now that Timothy chooses to tell Jenny that he'll be staying in Saffron. Jenny tells him that she's not sure if she can pick him over Reggie, he tells her that he knows she'll do what her heart tells her too.
The two find themselves in a place called Hidden Village where Flint is indeed rejuvinating himself. However he does not fight, he has been calmed by the village's caretaker Cindy. He tells them that Eustace did not send him here, in fact he hasn't seen Eustace in years. However he does not allow himself to be arrested without a fight. His new Graveller is not a ground type, it has been merged and forged to make it a steel type.
They aplogise to Cindy, she pleads with them. Begging that they let Flint stay here as he has calmed himself so much. Jenny and Timothy tell her that he's a murderer for hire, he worked for Team Rocket. Cindy still pleads however they continue through and try to take him to gaol anyway. However the trip back through the forest is even harder.
They continue through and find themselves at the edge of the forest however they are this time attacked by the disciples of Cindy. The forest children who are attacking them on the command of Cindy. They won't go down without a fight but Jenny and Timothy still defeat the children.
Just as the two police officers reach the edge of the forest they are confronted by Cindy, she pleads one last time before attacking the two. Once she is defeated she claims she is pregnant and cries, Jenny gives her the card of a lawyer and tells her that she can try to get Flint bail but the chances are he's going away for life. Jenny tries to be sympathetic, however she has a duty as an officer of the law.
Jenny and Timothy are praised for bringing in Flint and Marble and the other detectives have been released from hospital. Marble is thrilled to be back with her friend and Timothy is glad to be staying in Saffron. Marble and Jenny are assigned the case of the murder of Lina Jeffreys, when they protest saying that they should be working on the rocket cases Cheif Avery tells them this is a rocket case.
Lina Jeffreys is the granddaughter of Giovanni, her mother who was his daughter famously got away from Giovanni and helped bring down Team Rocket. Lina has lived a life under the spot light and is constantly harrased, it is suspected that she was murdered by a Team Rocket member trying to get even for Giovanni.
Marble and Jenny go to the crime scene where they see that it is clean, imaculate even and her body has been cleaned up. They've layed her out on the bed as though she were asleep. Most of the forensic evidence was gone from the scene.
Preliminary reports from the forensic investigator revealed that she was killed by a lethal injection with pokemon poison. A tactic very popular by early Team Rocket, pre-Giovanni Rocket and an ancient tribe from Cinnabar Island which was believed to have migrated to the Sevii Islands after Cinnabar Island was re-settled.
The two girls look up the old rocket on their files and try to find out who their leader was, their leader before Giovanni was mysterious and there are no records indicating who they were. However it does show that they didn't stand for world domination but for the freedom of the Cinab people which is why they used the pokemon poisoning.
The girls find that there is a Cinab support group in Saffron, they go to the centre and ask if they can have a list of the members of the organisation, they are denied due to privacy so they have to send Timothy who is part Cinab in under cover.
Under the guise of "Andrew" Timothy enters the group to find any suspicious seeming members, he finds one by the name of Dean. He seems to be a believer in the Cinab people reclaiming Cinnabar Island. To probe further Timothy mentions Team Rocket, Dean responds saying they were once great freedom fighters who turned their backs on their own people.
Timothy follows up with Dean after the meeting and asks him what he heard about Lina, he says that she was the descendant of the self proclaimed first King of Cinnabar and the Seafoam Islands and that what happened to her was Karma coming back for revenge against her lineage. Timothy is then invited to a getogether at Timothy's club, the police decide that they need an insider as Timothy's date preferably somebody of Sevii heritage, Jenny knows that Joy is of Sevii heritage so she asks her to be involved in the sting.
The two under the aliases of Andrew and Andrea the two attend the party and the mingle meeting Dean's date Leslie, who is wearing Lina's ring. Joy lures her into the toilets and knocks her out so she can get the contents of her purse, she finds a ledger displaying the plan of the assisnation of Mayor Sabrina, she takes photos of the plans and goes to find Timothy.
Jenny is contacted immediatly and put on security watch at Sabrina's mansion. There she remains until they are indeed invaded by the Cinabs, Jenny remains and defeats them all, she tells Sabrina that she has to get out of there, Sabrina reluctantly agrees but not before she teleports in Jenny's good friend Squirtle and then gets her Alakazam to teleport her out so when Dean comes up he finds Jenny alone and attacks her.
After he is defeated he breaks down and says that Eustace promised that he would win, promised that he would be able to become the mayor if he just killed Lina and Sabrina, he said it would be easy. He then goes to stab Jenny but Squirtle jumps out in front of her, his bravery makes him evolve into a Wartortile.
Dean is arrested and in exchange for only being charged with Murder and consipircy to commit murder instead of Murder, conspiricy to commit murder, organised crime attempted murder and conspiricy to commit crime leaving him with a life sentance with chance of parole in 20 years he spills all of the information he knows on Eustace.
Jenny tells Reggie about her cheating and he breaks up with her so she goes to Timothy and tells him to stay, she then pursues a relationship with him instead.