The story follows Kim and Ron in the period after "So the Drama", continuing the story as left off from the end of the movie, taking place an unspecified amount of time after.
The story begins with Kim lying asleep in her bed, dreaming of standing in an open field within an oriental country. Before she could get her thoughts, she's greeted by Sensei, the master of the Yamanouchi Ninja School, who informed her that Ron would soon be needed again, and would need to wield the Lotus Blade and that she and Ron had developed a bond, and to call him when the dream ended. Before she could ask or have any of her questions answered, the dreamscape ended and left Kim in her bed. Confused, she followed the advice and called Ron, who explained that Sensei had talked to him before and that it'd be better to speak later as it was 2:45 in the morning.
In the morning, Kim quickly dresses, briefly noticing her burnt prom dress and remembering the night before heading out to meet with Ron. Unusually, Ron was acting secretive and quiet. Briefly stopping to get breakfast, the two travel to the park and Ron explains that whatever it as had paled in comparison to the previous adventures involving Yamanouchi, and that now Kim needed to know. As Ron finishes, Yori appears, carrying the Lotus Blade concealed within a box. Ron undid two of the clasps, but left the third for Kim, who opened it after a brief rush of emotions and a sense of power from touching the clasp. Yori explained that Kim wouldn't have been able to open the box if the Lotus Blade hadn't accepted her to be at Ron's side, or hold Ron's hand while he was holding the sword. Yori then gave her a letter to read.
The letter was from Sensei, and explained that the wielder of the Lotus Blade had always had a trusted companion, a partner, and that Ron had accepted his destiny to wield it. What he asked Kim was was she willing to accept Ron as an equal if not a superior in order to follow what Sensei believed to be her destiny: to stand beside Ron. Placing the letter in the box which had contained the Lotus Blade to, as Sensei had said in his letter, accept, Yori then gave Ron the Lotus Blade's scabbard before also giving Kim a silver necklace with a jade amulet on it, explaining that it was meant to be worn by the closest ally of whoever the Lotus Blade was wielded by, and her hopes that she'd of been able to wear it. Kim initially rejects the offer, citing that she lacked any sort of powers (magic or otherwise), but accepts. Yori then reminds Kim not to put herself entirely in Ron's shadow, and that they would need to be together to face what was ahead before leaving. Ron points out to Kim that, while she didn't trust Yori or Sensei, he did with his life and more importantly (to him), Kim's life.
After this, Kim and Ron share a brief moment before heading home, stormclouds gathering in the sky.
Unfortunetly for the two teens, they weren't able to make it indoors before the rain began to pour. Arriving at Kim's house, they toweled off. Mrs. Dr. Possible commented on the necklace, and Kim explained it as the two having matching necklaces. The two discussed plans for the rest of the day, and were heading for the Middleton Mall. When they arrived, Ron confided that he had previously had romantic feelings for Yori before Kim kissed him.
Inside the mall, their arrival was noted loudly by Brick Flagg, much to Bonnie's disgust. Brick effectively tells Bonnie to walk away, explaining after that he was sick of being treated as a "side of beef" by her. Monique then arrives and talks to Kim within the Club Banana store, telling her just how much of an impact their new relationship had, especially given how it had been announced, commenting that the yearbook staff had gotten a picture of it. Outside, some of the football players are cheering and goofing off with Ron. Monique comments on how Ron was quite likely the only man out there who wasn't perturbed by Kim "round housing some goon out a window". Before leaving, Monique teases about the two looking for a ring.
By Monday, Kim's father had noted some of the strangest things. First, some of his research had been taken from his lab. When he went to file a complaint of what was to his knowledge theft by his peers, the director instead instructed him to take a few days off and explained he was reciving a promotion in light of a new, critical project taking priority over everything else. The director, he had noted, was also wearing indoor sunglasses and claimed that it was due to a drug they were testing that made their eyes sensative to light. Later, he went to check his computer and had also discovered that files were missing and removed. Before he could report this, two security guards intercepted him and escorted him out 'for his own safety' due to a spill and that they had handled it. In total, he'd been given three weeks paid vacation while the space center made ready for the new project and invited Ron to join the family in celebrating as he could now 'afford to feed him'.
However, Wade quickly called and explained that Doctor Director, leader of Global Justice, wanted to meet with her later. She was suspicious because of all the sudden changes in the space center and her agent within was saying that it was all fine. Wade also made mention of their new relationship, which they hadn't informed Wade off yet. When confronted on this, Wade explained that the Tweebs had known a man on the yearbook staff and then put the picture onto the internet, and it had gone viral quickly. Telling him to keep her posted, Kim and Ron got ready to head down to the local beach.
When they arrived there and had started moving into the lake, Kim quickly noticed it was colder than usual. A nearby man explained that it was the space center taking up more water for usage in their lab, as such the water was on average colder due to runoff. Playfully shoving Kim into the water, Ron sped across the lake as the two enjoyed their afternoon. On the other side of the lake, Ron dropped behind Kim and, acting on instinct, she quickly knocked him onto the floor with a judo move. Laughing it off, Ron returned the favor with a leg sweep and the two nearly share a tender moment when they notice a footprint. An inhuman, muck covered footprint that neither of them had seen since their last trip to Camp Wannaweep.
Calling Wade, he informed them that not only had Gill somehow broken free, but there had also been a major theft of genetic material and files that were used by DNAmy, leading Doctor Director to believe that there was something else at work. Returning to Kim's house to get ready for dinner, Ron accidently grabs the laser lipstick and, through an accidentally activated shot, winds up 'fixing' her burnt dress, which she planned on wearing. Before they could leave to go to dinner, however, Wade called and informed them that Doctor Director needed them ASAP as her agent on the inside had reported an accident before being cut off.
Moonflower:EditKim and Ron, missing the dinner planned in order to help, were dropped off outside the Middleton Space Center and were met on the way in by the Director, Randall Averington, who apologized for them being called on to look into the incident. He explained that it was an accident in one of the labs which resulted in chemicals spilling out, which injured the representative who was now being held in the security infirmary as was "standard procedure". They were then given a brief tour of the facility, Averington explaining that they had been testing new engines. When his assistant was asked about the GJ agent, the assistant explained that he believed that the agent had seen it and thought they were doing something to the reservior, and thus placed a charge in order to get close. Unfortunately, the charge detonated some of the fuel that was stockpiled there and resulted in a chemical leak. Unusually, one of the side effects of the chemicals was the incapability of individual thought, turning him into a zombie-like state. While he went to answer a phone call, Kim took some brief scans of the area with her Kimmunicator. When the assistant returned, they thanked him and left the facility. As they left, two figures wondered how much they suspected, and did not like how Kim and Ron had been looking around that area...
As they had missed the original dinner plan, Kim and Ron went to Beuno Nacho to get their dinner, Kim calling her parents to apologize. As soon as she finished, Wade called and told them that Doctor Director wanted to see them. Immediately, and was taking the two via cab to the rendevous point. Taking the cab that they had been directed to by Wade, they were driven to Doctor Director's mobile headquarters, where they met Wade in person as well as Doctor Director. Doctor Director explained that what was going on at the Space Center was not a unique case, several government sites had seen similar unusual occurances and even Global Justice's headquarters had a mole or two, leading to their meeting in a mobile headquarters. Doctor Director confirmed that part of what they had found in the Space Center was a scale from Gill, confirming their hunch that Gill was active after finding the footprint at the lake. Doctor Director also warned that Gill had seen another mutation since their last encounter and so likely possessed new mutagenic tricks.
Then Doctor Director explained that they needed to go back to the space center, and needed to do so covertly as she felt the Space Center was hiding something from Global Justice. They were to go in, find all evidence needed and then do whatever sabotoge they could and escape by any means possible. In light of Gill's likely presence in the lab, they were given some new equipment from Global Justice, including hardware they normally didn't use. High yield explosives disguised as juice boxes and more powerful than any explosive of that size.