An Asian man steals a bike outside a biotech company. Monk and Natalie are walking nearby and Natalie notices the thief when he rides the bike over a pothole and falls. Monk steps on something and asks for Natalie's help, but she goes to help the man instead. Despite the fact she sees his pair of bolt cutters, she doesn't think anything unusual is going on. As the thief rides away, Professor Dean Berry comes out of the biotech company and yells that his bike is being stolen.
Monk and Natalie go into the company and wait for Berry. They talk to his assistant Sarah, Longson, and she explains that they do agricultural research. Monk notices that they're working on square tomatoes to cut down on storage space. Berry comes in and checks on his experiment on fast-germinating seeds. Pleased with the results, he tells Sarah to call their investors and then locks the seeds up in a personal safe with a keypad combination. Natalie tries to buy him a new bike but Berry says it was a custom-made gift from an environmental gift. Natalie volunteers Monk to help find the bike, much to Monk's irritation. She's already called Stottlemeyer and Disher about the "emergency," and they arrive. However, Stottlemeyer isn't thrilled to learn she's called them in on a bike theft.
Back at his apartment, Monk is making sandwiches with a sample square tomato that Sarah gave him. Natalie badgers him into helping, noting that she's collected lots of "karma chips" from all the stupid things she's done for him above and beyond what he pays. He gives in and they go to the station to look for mug shots. They spot the thief, John Kuramoto, a known auto thief. They go to Kuramoto's home and Monk knocks on the door and asks for the bike back. Kuramoto fires through the door and hits Monk in the left leg.
At the hospital, Monk wakes up to discover that his arms no longer "match." Natalie tries to apologize but Monk isn't convinced. She explains that Kuramoto escaped and that Stottlemeyer is leading a personal search. Stottlemeyer and Disher bring in Kuramoto's cousin, Vince, who was staying at the house. All Vince knows is that someone paid John $3,000 to steal the bicycle.
Natalie brings Monk home in a wheelchair with no engine. She has to push him around and, guilty, promises to stay with him without asking for overtime pay. Stottlemeyer and Disher arrive and brief them on the fact John was targeting a specific bicycle. They wonder if there's something hidden inside the bicycle, and Stottlemeyer insists that Monk avoid self-pity and go with them to talk to Berry. They go to Berry's solar-powered home and (eventually) get him into his wheelchair and up to the house. Berry says that the bicycle has a honeycomb structure and no one could hide anything inside of it. He explains that an environmental group, the Visionary Project, gave it to him as a gift and Sarah brought it into the laboratory for him.
John Kuramoto goes to a cemetery to meet his employer: Sarah Longson. She pays him off and he hands over the item he stole. She asks for the gun he shot Monk with to dispose of it. Once she has it, she shoots him in the back as he leaves.
The police investigate the crime scene and Monk and Natalie goes there. Natalie is starting to collapse from all the extra works she's been doing for him and the lack of sleep. Stottlemeyer has confirmed that Kuramoto was killed with the same gun that Monk was shot with. The captain also has determined that the Visionary Project didn't send a gift to Berry. Monk spots an unusually-sized tire track and manages to fall out of the wheelchair when Natalie fails to keep an eye on him for a second. Stottlemeyer sends Natalie back to the car and then tells Monk that he's treating Natalie poorly and he needs to stop before he loses her.
Garbagemen find the discarded bicycle in a dumpster.
Natalie is pushing Monk up a hill on his errands and he wonders if she hates him for how he's treating her. She half-heartedly denies it but then finally collapses in exhaustion. As she sits there crying, she fails to notice Monk wheeling down the hill.
Stottlemeyer and Disher talk to the garbageman who found the bicycle. He explains that thanks to his knowledge of detritus, he can tell it was discarded 20 minutes after it was stolen. They still haven't found the lock.
At the biotech company, Berry is trying to replicate his fast-germinating seed experiment. It fails and can't figure out why. Sarah has to leave for her trip to China. Natalie arrives with the bicycle and Monk comes in a minute later in his new powered wheelchair. He ends up smashing around the laboratory and rolling over Natalie's foot. Berry is more concerned about Natalie's exhaustion and dehydration, and gets her some vitamins and juice. Monk finally realizes how she's suffering and offers her an apology and a wipe. They prepare to go and Berry comments that the lock is missing. Monk remembers they never found a lock and asks for a description. Berry says that the lock had a keypad combination. Noticing Sarah packing, Monk asks where she's going and realizes that Sarah sabotaged Berry's experiment. He explains that Sarah planned to steal the seeds to a buyer in China. She needed to get into Berry's safe so gave him the fake gift, with a keypad lock he could set. She designed the lock so she could obtain the combination, figuring Berry would use the same combination as his safe. Then she hired Kuramoto to steal the bike, ditch it, and bring the lock to her. Once she recovered the seeds, she would disappear to China and sell the seeds for big bucks. Sarah points out they have no evidence, but Monk has noticed that she wears sandals recycled from tires… and her sandal print matches the "tire tracks" at the cemetery. Sarah makes a run for it and Natalie goes after her. Outside, they struggle and Natalie manages to grab the gun. She orders Sarah to surrender, but when she turns toward Monk, she shoots him in his other leg. At the hospital, Monk wakes up in extreme pain, asks for her karma chips back, and she tries to comfort him noting at least now his legs match.