Team Rocket Trio

Beginning of the story
Jessie and James are the only two members of the team remaining. They both have connections to team rocket but work independently.

In the past
They became heroes of the organization by doing something important, but later James decided that he was done with the team and abandoned them. Jessie followed, but kept ties and helped from time to time, to James' dismay. Meowth followed his friends, but was eventually kidnapped.

During the first half of the story
The two are looking for Meowth and his whereabouts. They believe he was captured by a group of scientists, who approached him in the past to help them understand the cursed pokemon (as he can speak human language). HOwever, when they suggested that he succumbs to the curse so that he tells them what it is like, he refused.

The scientists didn't say much back then, so Jessie and James don't have much to go on. Even the fact that they took him is a theory. However, the scavenge the free cities looking for lists of former scientists who might be working on a project that involves meowth. Team rocket connections have helped, but under the radar mostly, as they haven't ruled out the possibility that a rocket branch could be responsible.

In the end, Meowth was kidnapped by Devon corporation. Devon corporation is heavily associated with Team Cipher.

Meowth's rescue attempt
Eventually, J&J locate meowth and storm New Island to rescue him. They find out about the project of Devon corporation and with help they fight Looker and Steven (two extremely powerful trainers). They both fight against Looker in a double battle, while Gary Oak fights against Steven, former champion. Giovanni, who has also joined the raid, is battling against Mr. Stone, Steven's father.

After they barely win the battles, it is revealed that Meowth has been changed by a DNA-altering formula that was created by Devon Corp. This formula takes the DNA of a meowth from another region, and applies the differences to Meowth of Kanto region. This way, the DNA of meowth changed to Alolan Meowth, which made him dark type, therefore succumbing to the curse. This all happened because Meowth didn't accept to submit to the curse.

During this time, J&J wanted to kill him to finally give him peace, as this creature was nothing like what their friend used to be, but the other trainers there chose to use psychic pokemon and purifying techniques to get into Meowth's head and get some answers for the curse. Vergil didn't care, which enraged J&J, but afterwards they understood, and during the process Meowth's true self returned and fought with his cursed self, but eventually lost. He told them that he can't be saved, and pleaded with them to kill him as it was torture to be sane inside this body. He also said that "he hears his name", referring to Cole, and implying that all cursed pokemon hear his name. He doesn't name him though. He gives info about the curse for as long as he fights to win his cursed self, but eventually disappears forever. The cursed self then threatens them and says they don't have any chance of winning, and allows real Meowth to surface for seconds, only to show them that he is torturing his soul.

In the end, Ash arrived to put meowth out of his misery and scolded Vergil for doing this. Vergil retaliated saying that Misty was murdered by creatures like this and he doesn't feel sorry.

Aftermath
After losing their friend, Jessie and James were traumatized. James wanted to take Jessie to his old house, retire and live there peacefully as long as they can, while Jessie wanted to go back to team rocket actively again. This caused a friction in their relationship, and they eventually broke up.

Battle of Saffron
During the battle of Saffron, Jessie and James are assigned to side with Giovanni, leading an attack from the west (most probably). As a result, they are far away from the ambush, and this is what Giovanni intended. He took the two on a cliff, from where they could see far, and they witnessed the ambush together. However, he prevented them from going to assist their allies, and explained what the secret plan he made with Ash is. He told them they are like children to him, and wishes for them to willingly join the dark side and join him, Ash and Delia as family. He promised all the hurt and sorrow would go away once they do, but they refused, remembering what Meowth said. He said he feels sorry about Meowth, but he couldn't stay alive or he would be at risk of exposing everything. Jessie and James refuse, and he says it's too bad they are so short-sighted. He says that nothing goes above the plan, even his own children, and he will kill them if they won't agree.Then a double fight occurs in which Giovanni loses and is killed. Jessie and James decide to go help anyone they can, and they help save some people, mostly team rocket grunts, but also Cole who is injured.

Post-Saffrom Story
Jessie and James run back towards Celadon, where team rocket has the resources to hide and get away. Both are sure that Ash and the forces of darkness will come after them. Shocked at the fact that they just killed their boss, and person they worshipped as a father, they hesitate to tell anything to the other members who are still in the dark. Jessie is thinking to lead the remnants of team rocket, while James wants to live out his remaining time with Jessie.

Jessie, James, and more than a hundred grunts and officers are holed up in an old warehouse, where they are safe for the moment.

Grunt1 (will eventually get a name): Commander Jessie, where is everyone else? Where is the Boss?

Jessie stays silent for a bit. "Giovanni is dead", she replies, her voice trembling with shock, as the previous events seemed like a nightmare she would soon wake up from.

Another grunt interrupted: "What? How did that happen? How is the boss dead and you are alive?"

James intervened: "He died so that we could survive and come save you. Ash betrayed us all. The whole plan was a trap. Boss Giovanni saw that, and sacrificed himself so that we could escape, so that we could come save you. Let's all leave soon. Disperse, go anywhere, find the people you love, or stick with them, if they are on this group. And wait for what is to come. We lost today. We survived, but we can't stop what's coming now. There is no team Rocket anymore".

"No", Grunt1 interrupted. "We are still team Rocket, we are a family, and the boss was our father"

"Yeah", many others exclaimed.

"A father may die, but the family remains a family. All my brothers and sisters are in this room. I am not going anywhere"

The crowd cheered and applauded.

"Even if we have lost, even if we die tomorrow, we can still fight together to the end. I don't care to go hide somewhere among other people. I never cared about other people. We may have been criminals, but whoever wears this uniform still, they are my brothers and sisters. Commander Jessie, you can lead us. Commander James too if you want to come back."

The crowd cheered once more.

James sees Jessie tearing up over the kind words. "You are not thinking of leading them right?", he whispers.

"They are my family as much as I want you to be too. Can't leave them", Jessie replies.

James gets up from next Jessie and calls out to the crowd. "I killed Giovanni", he says coldly.

The room stays dead silent for a moment, until Grunt1 breaks the silence.

"Why would you say that?", he asks. "You are so kind that you wanted to leave team rocket, there is no way you would kill the boss", he added.

"Ash Ketchum betrayed us", James continued without paying attention. "And boss Giovanni was Ash Ketchum's father. They betrayed us together", he concluded.

"Stop saying these lies", one grunt threatened as he reached for his pokeball, but felt Jessie's Yanmega's sonicbook toss the pokeball away.

"Just whaat the hell are you think you are doing James?", Jessie asks, for the moment finding her strong and confident personality.

"Saying the truth, checking to see if they are really a family, our family", James replied. "Giovanni betrayed us, betrayed you actually. He wanted to frame the killing of all those trainers to team rocket, while he offered Jessie and me to join him on the dark side, with Ash. This is how much of a family you were to him", he concluded.

"Shut up", the same grunt as before shouted, attacking James and punching him tot he floor.

Blood came out of James' mount, but he ignored it. "I am planning to leave this place alive with my family, my Jessie, and live whatever little time I got happy. That's all i ever wanted. I only ask of you to let us go, and do whatever you want after. I don't want to hurt anyone, but if you get in the way of me and Jessie leaving, I will", he concluded with a threat.

Grunt 1 spoke again: "So why didn't you accept? If boss, in his twisted way loved you as children and offered you to join him, and you also know Ash for so many years, why not accept?"

Jessie: "Because you are my family, and I am James'. I chose, we chose, you over them. Sorry James, you were right to tell them the truth, I shouldn't have tried to take over by hiding what really happened. But now, I want to believe that team rocket is still here and still a family. I will go with James. But I also want to take with me whoever still feels like team rocket. Those of you who don't believe me, you can go or try to make us pay, if you think we were wrong to fight and kill Giovanni. But I don't want to fight any of you". She then grabs James' hand.

The crowd stood still, no foot moved from the ground to leave, no hand reached out for a pokeball to fight. Grunt1 spoke again: "I believe you", he said. "Somehow I do. Commander Jessie has been treating us like her children all along. There is no way she is lying now. I will follow you and commander James if you accept me".

Everyone nodded, some even yelled "yeah". Even the grunt who tried to attack James before nodded and accepted. Jessie was moved and in tears, and turned to James for approval. She knew he wanted the two of them to become a family, settle down and have children. This is nto what she was offering him.

James looked into her teary eyes, where finally the love and compassion for her comrades was showing. And he remembered that this is why he fell in love with her in the first place. "Very well", he nodded and smiled.

The crowd cheered and lifted their fists up. The new team rocket family was born.

Guerilla tactics
Soon after, Team Rocket used the death of Celebi and the abilities of Erika and her pokemon to take sanctuary in the former Celebi forest. Branded as a terrorist organization by the rest of the world, they relied on guerilla attacks to acquire supplies, and constantly moved base in order to escape capture by Ash's forces.

Cole remained with them for quite some time, during which time he trained excessively and grew much stronger. He even had a FwB relationship with a fellow trainer.