In the middle of being blasted off again, James finds a bottle cap from his training days that starts everyone reminiscing about being Team Rocket trainees. Jessie was a problem trainee, unable to work with any partner for long. Meowth walked into Giovanni's office, asking to be made a Team Rocket field agent. And Butch and Cassidy were trainees, too—Cassidy was Jessie's constant rival. Drill Sergeant Viper ordered Jessie to start training with her new partner, James, and Meowth was assigned to their team after Giovanni lost patience with its incompetence.
In their first team challenge, they had 24 hours to reach a target location in the wilderness, surviving on a loaf of bread and bottle of water per person. When Meowth ate all its food right away, James shared his food with Meowth. Jessie sniffed at such sentiment, but when they made camp that night, she reluctantly shared her own food with the other two. The next day, the trio had to cross a rickety bridge. Jessie made it across, but the bridge collapsed beneath Meowth and James. Although Jessie grabbed them just in time, James let go and fell into the river below, thinking it was for the best. His injuries put him out of action for the final trainee test: a real heist job to steal a red Snorlax from an office tower.
But to Jessie's surprise, James showed up for the mission anyway. Nothing would keep him from being there for his team! The only teams left were Jessie, James, and Meowth against Butch and Cassidy; in the final room, Butch and Cassidy fell into a pit trap, and James and Meowth almost fell in as well. This time, Jessie grabbed her partners and wouldn't let go, even when the building's alarms went off. As soon as she pulled them to safety, they started to make off with the Snorlax, but time was up—and the Snorlax was Drill Sergeant Viper in disguise!
Not only did Butch and Cassidy pass, but Jessie, James, and Meowth also become real Team Rocket agents for getting as far as they did in the final test. Back in the present day, Team Rocket is still blasting off after another failure, but no matter what, they're still a team!
During yet another blast-off, Team Rocket remark that this situation is becoming rather familiar. To save a hard landing, Jessie orders James to get the emergency floatation device out. He rifles through his pockets, but only pulls out some of his prized bottle caps flying One of them, a beat-up gold one with a red R on it, lands on Meowth's face. James looks at it closer and remarks that he has kept ever since their days at the Team Rocket Academy. Jessie gets very sentimental, and a flashback begins.
Jessie recalls a training exercise where she descended downwards to snatch a giant Articuno statue. Looking up, she sees her partners, Jubei and Mankey, struggling to hold the rope. Back to the task at hand, she wraps her arms around the statue and tells them to pull her and the statue up. Suddenly, the rope slips, and Jessie drops the statue, causing it to shatter on the floor and triggering the security system. Jessie drops to the ground and exits out a door, Jubei calling after her though she ignores him and leaves. The room collapses on him and Mankey. An automated voice announces that the test is complete. Drill Sergeant Viper tallies up the score, and asks Jessie to explain why she has now lost her tenth partner in two months. Jessie remarks that Juei wasn't good enough, like the others.
Later, Viper reports to Giovanni the results of the training. He remarks that Cassidy, Butch, and their Raticate are performing well. He looks over his charts and sees that the top contenders in the Red Team were rejected except for Jessie. Suddenly, a grunt bursts in the room, telling Giovanni that his unit discovered something rare: a talking Pokémon. At that point, Meowth appears, saying that he wants to join Team Rocket. Giovanni's Persian looks jealous of Meowth, who is on the floor eating ravenously from a bowl, talking to Giovanni as he eats. Giovanni simply remarks, "I see," without making further comment.
Meanwhile, Jessie and Cassidy are running on treadmills; they glare at each other and begin seeing who can run the fastest. As a result, both treadmills break down. They both retire to the locker rooms, where they begin exchanging insulting insults. Cassidy wonders who Jessie's new partner will be. At the end of the conversation, Cassidy calls for Butch by the wrong name over the wall to the male locker room; he yells at her that she got his name wrong. Jessie is left feeling deflated, but later she gets some news from Viper – she has a new partner. He points to a nearby wall, against which James is leaning. Both trainees glare at each other and speak cautiously. James tells Jessie that he has never run away.
The next day, Jessie and James are put through an agility and endurance course together, jumping over pits and barriers. While crawling under barbed wire, they stop and glare at each other before continuing on. Jessie manages to run over a group of hole traps without falling in, but James falls into one. Jessie stops and looks back to tell James that she won’t be waiting for him. James climbs up by himself, saying he won't run away because he never has. Both trainees begin running again.
Meanwhile, Giovanni is becoming annoyed with Meowth and his behaviour, and places a call to get rid of him. Meowth returns from a disastrous coffee run, returning to Giovanni's office, burnt and disheveled. Giovanni calls him over, and Meowth responds enthusiastically, hoping he can replace Persian as Giovanni's pet. However, Giovanni has other plans. Later, Viper introduces Meowth to Jessie and James, telling them he will be their teammate. They look skeptical at first, but are shocked when they learn he can speak human language. Meowth thinks he is special because Giovanni gave him a job to do.
The Team Rocket hopefuls face another skills test. Viper shows a group of teams a mountainous map with an X, telling them to reach that point in 24 hours with a supplied loaf of bread and bottle of water each. Jessie and James exchange unsatisfactory glances again before setting off. In the hills, the teams are seen hiking over rocks. Meowth stops to eat some bread and drink before cooling himself with his remaining water. As Jessie and James prepare to swim across a river, Meowth admits that he cannot swim, so James carries him across the water on his head. While scaling a rock, Meowth slips down, James having to aid him again, giving him some of his water and bread on one condition- he returns the water bottle's cap. Jessie looks back and keeps climbing the rock.
Nightfall, and the three are around a campfire, James and Meowth appearing to sleep. Jessie pulls out her bread and water and hears Meowth's stomach growls. She almost eats her bread, but instead splits it into three parts, giving one to Meowth and one to James. He originally resists, but she tells him that "we eat together as a team." He takes the bread. Sometime later, the campfire is out and the trio appear to be sleeping. Meowth is snoring loudly. Turned away from each other, James asks Jessie if she's awake, and she answers "yeah." He confesses to her that his remarks about not running away were lies, and that he has been running away his entire life thus far. She then confesses that she has always been alone and has never felt friendship or love. Both say they are optimistic about tomorrow, and vow to be the top team. Meowth agrees in his sleep.
The next morning, the three find that they have to cross a rundown rope bridge. Meowth is scared, but Jessie tells him that they are a team and have to go together. James gives Meowth a pep talk, and Jessie continues ahead onto the bridge. A plank falls out ahead of her, but she misses the gap and keeps going. She eventually makes it across the bridge safely. Then, James attempts to cross with Meowth riding on his head. Suddenly, a rope holding the bridge up breaks. Jessie reaches out to them, but all James can do is throw Meowth to her while holding on to his tail. Seeing that Meowth is in pain, James lets go, dropping into the river. Jessie screams for him. Later, Jessie and Meowth are standing outside an operating room with a doctor while James lies completely bandaged from his injuries. Jessie and Meowth are upset, but decide to continue with their Team Rocket training.
Viper announces to the remaining recruits, Jessie, Cassidy, and Butch, that today they will be facing their ultimate and final test. He explains their mission; to retrieve the Red Snorlax statue from the top of a tall penthouse, but there are many traps waiting for them. The first team to steal the item and flee into the waiting helicopter becomes the top team. Later that night, Jessie and Meowth appear in some bushes alongside Cassidy, Butch, and Raticate. Cassidy and Butch go ahead, scaling the skyscraper's walls using suction cups. Back in the bushes, Jessie walks off, about to give up, remarking that loneliness is the story of her life. Suddenly, James appears, still bandaged. He says the first couple of lines from what will soon be the team's motto, and pulls the bandages off, apparently unscathed, to a shocked Jessie and Meowth. He tells Jessie that he doesn't want to run away this time. Jessie's eyes well up with tears, which she clears, and the three rush off to beat Butch, Cassidy, and Raticate.
After making it through numerous traps, both teams enter the penthouse with the red Snorlax from opposite doors at the same time. Cassidy and Butch run ahead to the Snorlax, Cassidy actually calling Butch the right name this time, but a hole appears in front of them and they fall in. Jessie tries to stop her own teammates from doing the same, but James and Meowth run ahead and fall into another hole. James grabs onto Meowth's tail again, and Meowth manages to hook his claws onto the floor above, but the two begin sinking quickly. Jessie runs up and grabs Meowth's paws. As the security alarm sounds, James tells Jessie and Meowth to go on to be a good team, leaving him behind. Jessie tells him she hates that idea, but James lets go of Meowth's tail anyway. Both Jessie and Meowth manage to grab onto his hand before he plummets. James tells them to let go, but they refuse. James is visibly touched. Finally, Jessie and Meowth pull James out of the hole and turn their attention back to their mission. They make it to the caged Snorlax and activate a balloon that raises it to the ceiling. An alarm clock rings and Viper emerges from the Snorlax, which was a costume. Viper announces that the results will be revealed tomorrow.
The next day, Jessie, James, Meowth, Cassidy, Butch, and Raticate stand before Viper, with the latter three in bandages. Viper tells the teams that despite the fact that they didn't capture the Snorlax, they have both been made official agents of Team Rocket. The two groups cheer in excitement and hug their respective group members. Jessie reflects on that day, remarking that they vowed to be the biggest and nastiest Team Rocket team in history. While Jessie remarks that things haven't really gone that way, James remains more optimistic about the future. James and Meowth state that being evil is a full time job, and Jessie's Wobbuffet appears just in time to add his obligatory agreement. Jessie's hopes are renewed, and she leads her teammates into a cheer for another Team Rocket blast off.