Both Lois & Reese head in opposite directions, Lois goes on a search to Kabul to find Reese and Reese himself deserts the Army.
The episode begins with Hal going over the recent events in his life; he was wrongly arrested thanks to his company framing him for embezzlement causing Lois to have a nervous breakdown and also get fired. As if this wasn't bad enough, Malcolm stole Reese's girlfriend causing Reese to join the Army under a pseudonym and now no-one has any idea where he is. The girl scout seller is asking him for money because she is there to sell cookies and not to hear about his life stories.
Hal is seen doing his fatherly duties when Malcolm asks if Lois is coming back from the Army recruiters. This is answered when he and the family hears her yelling at the army recruiters who brought her back. After Lois goes inside, one of the recruiters explain to Hal that she was being very volatile in attacking them with her tirades and demanding to know where Reese is. It escalated to having her attack them in the groin area, the recruiters had to arrest her and take her back home. Hal tries to bribe the recruiters to drop the case on Lois with the little money he has left to avoid a potential lawsuit in which the family can't afford. The men refuses to take the bribe and informs him that if she attacks them again physically and with her tirades, they will likely have her arrested again and she will be locked up in jail. When they leave, Malcolm asks Lois if she's ok. She answers in her angry tirades that she's not and explains that the recruiters won't divulge in any information to Reese's whereabouts, despite her explaining that he's underage. Lois mentions that the only way the Army can help is if they can provide the name Reese joined under, which they don't know, and even then it'll take six months minimum to find him. She mentions that the family can't wait that long because she wants him home ASAP. Hal tries to calm her down, but Lois remains angered by the lack of progress. She points out doesn't trust the recruiters to help her find Reese, so the family must do their part to find him. Since Lois doesn't trust the family to help her find him, it means she must find Reese by herself. This concerns Hal because he knows how things would turn out given how stubborn and controlling she is. Malcolm is also worried due to Reese's knowledge in using a gun from last time and that her rage is making things worse. He tries to convince Lois to calm down and focus on finding the name that Reese used to get into the army without their knowledge. Once the family have it, they could focus on finding him and getting him home sooner like she wanted. In her furious fit, Lois reminds Malcolm that it was his fault from the beginning for stealing Beth away from Reese that lead to the mess the family is in. Hal convinces Lois to go easy on him because Francis had already disciplined him for the earlier deed and conserve her wrath for Reese when or if they find him at all. She calms down enough to agree to the plan.
Hal decides to go down to the recruitment office himself and has more luck, learning that Reese signed up under the name 'Jetson'. However the army recruiter makes the service sound so desirable that Lois has to stop Hal from signing up himself.
Reese abandons the troops upon arrival in Afghanistan. He wanders around aimlessly and ends up dressing as a woman and getting himself married to an amorous man (with Reese later stating that finding out his bride was a man wasn't the deal breaker Reese thought it would be). Fleeing, Reese ends up wandering through the desert is at the point of giving up until Mr. Waffles appears as a mirage and encourages him to get home at once just to have good waffles again. Reese is unsure until Mr. Waffles reminds him that people in Afghanistan don't know what breakfast is since they simply stew up rice from the night before and pretend it's breakfast. He also informs him that his new waffles have more blueberries that plump up in the batter which makes them juicier. His words motivate Reese to stand up and put all his remaining effort and strength into getting home. Reese attempts to escape through car, boat, camel and turtle to get back home.
Further guilty for his actions, Malcolm decides to volunteer at a V.A. hospital. His boss there, Nurse Peterson, informs him on what day and hours he must give the medications to the elderly charges. She mentions to Malcolm that under no circumstances he can take them out of their medications, but refuses to explain why.
Lois heads down to the boot camp where Reese was previously sent and meets Sgt. Hendrix. After recognizing Reese as Private Jetson due to her showing him the picture, the two discuss disciplining children. Sgt. Hendrix is so impressed by Lois that he leaves the file about Reese in the open and lets her know he's about to look away from her direction. Getting the information she needs, Lois sells the family car and flies off to Kabul despite Hal's pleas.
At the V.A. Hospital, Malcolm decides to throw the pills out believing they were the source of their misery. Nurse Peterson reprimands him for the deed and this yields predictable results with the elderly fighting. While calling security to deal with the issue, she explains that the chaos and fighting is what the hospital were trying to avoid. Nurse Peterson tells Malcolm that he broke the one rule that she explained in the job earlier: Don't take the elderly veterans off their medications. She mentions those meds were needed to keep them calm and civil. Realizing his mistake, Malcolm tries to calm the elderly veterans down to predictable results.
At home, Hal picks him up from the V.A. Hospital and reprimands him for making things worse. He mentions it's bad enough that Lois is going against his advice and left town to search for Reese. Rather than come up with a snarky insult, Malcolm apologizes to Hal for the behavior. Hal mentions that he can be forgiven for trying to ease the guilt over his actions. It does little to comfort Malcolm and he heads to his room that he now shares with Dewey. There, he admits that he's a horrible brother. Dewey comforts Malcolm and wisely counsels him that they're going at it the wrong way. Reese wasn't the kind of person who helps others, he was a troublesome delinquent who loves causing mayhem and getting into all sorts of trouble. Dewey suggests they go to an art fair and honor him properly by doing all sorts of mayhem that he enjoys. Malcolm takes this to heart and they go to a local art fair to properly honor Reese.
Reese is found in small town in India, making an insult to the Hindu God, Hanuman. Despite his threats, Reese is face to face with Lois and is relieved to see her at first. He may regret his relief sooner. Lois thanks the local men helping her find Reese and they leave. She proceeds to yell at him for causing their family grief in illegally joining the army and almost getting himself killed in going AWOL over the heartbreak he had endured from his girlfriend dumping him. Lois mentions that Reese is going to be grounded for such a long time as she drags him by the ear home to California.
On top of a roof overlooking the art fair, Malcolm and Dewey solemnly launch diaper-balloon bombs (filled by Jamie) over the unsuspecting patrons. They go over the times Reese had tormented them with his mayhem. Malcolm is solemn knowing that likely Reese is going to be gone for a long time and that sharing a room with Dewey will be much harder on him. Without him causing the family mayhem, Malcolm would likely be unable to come up with ingenious plans and Lois will continue blaming him for the departure. A newly arrived Reese surprises them on the rooftop. After an admittedly warm and fuzzy reunion hug, he reclaims his place in the community, launching another diaper-balloon upon the folks below. The boys are back, indeed.
- Jane Kaczmerek as Lois
- Bryan Cranston as Hal
- Christopher Kennedy Masterson as Francis
- Justin Berfield as Reese
- Erik Per Sullivan as Dewey
- Frankie Muniz as Malcolm
- Steve Rankin as Sgt. Hendrick
- Caroline Aaron as Nurse Peterson
- James Black as Sgt. Rick
- Drew Massey as Mr. Waffles(voice)
- Matthew Atherton as Military Police
- Larry Marko as Ed
- Farrah Grey as Flight Attendant(credited as Farrah Skylar Gray)
- Sunny Bedi as a tribesman
- David Kavandi as Mullah
- Luke Bayback as a teenager
- Emma Lockhart as Girl Scout
- Matthew R. Anderson as a paratrooper(uncredited)
- Paul Michael Bloodgood as Recruiting Officer Dorn(uncredited)
- Dave Powers as Private James(uncredited)
- Wells Rosales as Private Martinez(uncredited)
- Nicholas Roy as Private Franklin(uncredited)
- First episode to air in high definition.
- Reese gets legally wed to an Afghan man, while he is wearing a burka in disguise and posing as a woman. He never technically got divorced with this man, but he did run away from him. In the later episode, Bride of Ida, Reese would get more officially wed to a girl named Raduca. This would technically making Reese a polygamist, until the episode College Recruiters, where Reese and Raduca would get divorced.
- It has been theorized that when Reese says that his husband didn't mind when he found out he was a guy, there was a possibility that something that was not completely consensual happened between them.
- Under the military code, Reese going AWOL upon arriving in Afghanistan could have resulted with him receiving a dishonorable discharge, forfeiture of all pay and a confinement of up to of 5 years in federal prison. To make matters worse, if the Army found out that Reese used the false surname Jetson earlier, he would be considered a military impostor and would also result in imprisonment.
- Reese is seen getting punished by a group of Hindus for making fun of one of their religious deities. Reese claims that he only made fun of it because he looked like a giant monkey man. This may have been a reference to Hanuman.
- Francis and Piama do not appear in this episode. It's presumed that they returned to New Mexico and their lives at the Grotto ranch.
- This marks the 4th time Lois had been arrested. The first three times are in Traffic Ticket, Book Club and Monkey. Her final time being arrested is in Halloween
- This is Steve Rankin's final appearance as Sgt. Hendrix
- This episode marks the final time that a cold opener has deviated from most of the cold opener in which one plays a significant role in the story itself. The first time was in Emancipation. The 2nd time is in Humilithon. The 3rd time is in Day Care. The 4th time is in Reese Joins the Army: Part 2