An Asian man is walking downtown, approaches a bike rack, and steals a bike. Meanwhile, Monk and Natalie are walking nearby and Monk is panicking because he stepped on something. As the thief rides by, he hits a rock and falls down, and Natalie comes to his aid. He quickly rides off as Professor Dean Berry runs out of a nearby building and chases after the thief, accusing him of theft.
Monk and Natalie go into the building and talk with the victim's assistant, Sarah Longson. She's glad that nobody was hurt and explains that they do agricultural research. Monk is intrigued by the fact they're developing square tomatoes. Sarah introduces them to Berry, who is busy working on an experiment with fast-germinating corn seed. He tells Sarah to call their investors and then talks with Natalie. He's less than sympathetic with her claims of innocence and locks the seeds up in a special safe that only he knows the combination for. Natalie offers to buy him a new bike but he says it's irreplaceable because it was custom-made, had a cool lock, and donated by an environmental group. Natalie commits Monk to finding the bike and Stottlemeyer and Disher arrive in response to her call. Stottlemeyer is less than thrilled to be called in on a stolen bike case. They go over the security monitors and watch the crime, and Stottlemeyer sarcastically offers to call in the bike squad.
Back at Monk's apartment, Natalie admits that she has no idea how to find Berry's bicycle. Monk is busy cutting up the sample tomato and enjoying the taste. Natalie badgers him into taking the case, cashing in her "karma chips" based on all the stupid stuff she's done for him. He agrees and they go to the police station to examine mug shots and try to identify the thief. They finally find the man, John Kuramoto, with two convictions for auto theft. Monk wonders why he's stealing bikes. They drive to Kuramoto's home and Natalie spots the bolt cutters outside on the porch. Monk knocks on the door and asks for the bike. The person inside shoots through the door and one shot hits Monk in the left leg.
Monk is taken to the hospital where he's upset that his legs no longer match. Natalie tries to apologize and explains that he has exactly 100 stitches, and brings him 100 daisies. Monk's doctor, Levinson, comes in and assures him he'll be fine. Monk isn't comforted and Natalie tells him that John Kuramoto escaped. Levinson notes it's unusual that someone would fire shots over a stolen bike. An angry Stottlemeyer is leading the search for Kuramoto and talks to his cousin, Vince Kuramoto, who is staying with John. Vince has no idea where his cousin is and Stottlemeyer points out he could be charged as an accessory. Vince explains that someone paid John $3,000 to steal the bike.
Natalie brings Monk home in a wheelchair and wheels him to the window. She tries to get him to look on the bright side without much luck and Natalie guiltily promises to stay with him and she won't ask for overtime. It's payday and he claims he can't reach his check. Stottlemeyer and Disher visit and tell Monk what happened, that John Kuramoto was stealing a specific bicycle. Natalie doesn't remember anything unusual about the bicycle and the others think there may have been something hidden in the bicycle. Stottlemeyer insists on taking Monk along with them and not letting him sit around and wallow in self-pity. They go to see Berry at his solar-powered home and eventually get Monk out of the car and into his wheelchair. They wrestle Monk up the stairs only to discover that nobody's home. Berry drives up in his solar-powered car and offers to adopt Monk some Brazilian rain forest in his name as a tribute to his sacrifice. He has no idea why someone would pay $3,000 for his bicycle, and notes that there's no way anyone could hide anything inside. He explains the bicycle was a gift from an organization called the Visionary Project, and his assistant brought it in.
That night, John Kuramoto goes to a cemetery to see his employer... Sarah. She pays him off and tells him he's going to have to disappear for a while. He gives her the item he stole and she asks for the gun he shot Adrian with. As he leaves, she shoots him dead.
The murder is reported and Natalie takes Monk to the crime scene, tired from everything she's been doing for him. He guilts her into staying with him and Stottlemeyer asks how she's doing. They confirm he was shot with the same gun that was used on Monk. They checked with the Visionary Project and the foundation has never heard of Dean Berry. Monk has Natalie point him in the proper direction and he finds a tire track. Monk falls out of the wheelchair and Stottlemeyer sends Natalie back to the car. He gets Monk into the wheelchair and tells him to ease up on Natalie. Stottlemeyer admits he knows what Natalie is going through because Monk is acting like him.
Garbagemen find the discarded bicycle in a dumpster.
As Natalie wheels Monk along the sidewalk, he wonders if she resents him. She denies it and he explains that Stottlemeyer is concerned. She finally collapses in frustration and asks him to forgive her. While she's talking, Monk wheels down the hill out of control and she finally notices and chases after him.
Stottlemeyer and Disher check out the bicycle and the garbageman explains that the bicycle was discarded twenty minutes after it was stolen. Stottlemeyer concludes that the thief stole the bike and also immediately got rid of it. The bell, the cable, and the lock are missing, but the garbageman finds the bell nearby.
At his laboratory, Berry is unable to replicate the rapid-seed germination experiment. As he leaves, Sarah smiles in triumph. He can't figure out why the experiment failed, and Sarah says that she has to leave for her trip to China. Natalie and Monk return with the bicycle and Sarah looks on in horror. Monk is in a new powered wheelchair but can't get it to work. He ends up going out of control, banging into desks and running over Natalie's foot. Natalie tiredly apologizes and Berry goes to her aid. He discovers she's dehydrated and suffering from sleep deprivation and malnutrition. Berry goes to get her some juice and vitamins, while Monk realizes what he's been doing. He offers her a wipe and apologizes for being a jerk. As they go, Berry says that his bike was locked and Monk remembers they never found the lock. Berry describes the lock and Monk realizes it had a key pad just like the one on Berry's safe. Monk notices Sarah preparing to leave and then explains that Sarah sabotaged Berry's experiment.
Here's what happened: Sarah planned to sell the genetically-altered seeds to her contacts in China. She needed to get Berry's combination so she gave him a fake gift with a combination lock that Berry could set, and that she could determine later. He used the same combination for the bicycle lock as for his safe. Once he set the lock, Sarah hired Kuramoto to steal the bike and give her the lock. She retrieved the combination, got into the safe, replaced the genetically-altered seeds with ordinary ones, and planned to be gone before anyone discovered anything. Sarah denies the accusation but Monk notices that her sandals are made for recycled tires. The treadmarks match the tire tracks in the cemetery. She throws liquid in Berry's eyes and makes a run for it. Natalie goes after her and manages to grab Sarah's gun, while Sarah grabs a rock. Monk hops after them as Sarah drops the rock and surrenders. Natalie turns around... and accidentally shoots Monk in the right leg.
Later, Monk wakes up in the hospital again with Natalie at his side. She notes that now his legs match.
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