Archer must salvage a crashed plane in the Season 6 premiere.
As Archer (more or less) carries out his mission, the rest of the crew formerly known as ISIS (minus Krieger) arrive at their newly renovated office, courtesy of Cheryl and Pam. Malory in particular is overjoyed at the office's new, futuristic look, only to find that it was all a holographic simulation disguising the true office, a faithfully recreated version of the old office (minus the ISIS logo, naturally). The only addition to the office seems to be a robot named Milton, a copier-shaped toaster.
As Archer traipses through the jungles of Borneo, he's ambushed by a Japanese soldier named Sato Kentaro, who has been out of touch with the outside world since the 1940's. He believes World War II is still going on and as such, treats Archer with hostility. Using his phone, Archer tries to convince Sato that the war ended, but to little avail. Archer is then forced to take Kentaro prisoner as he continues his mission.
Back at the office, everyone is baffled to find how thoroughly the ISIS office was recreated, right down to the most minute details. Apparently, Cheryl had the aforementioned recreations done as a joke on Malory.
Back in Borneo, Kentaro leads Archer into a trap, wherein he skewers his foot on bamboo. Hearing guerrillas approaching, Kentaro attempts to flee but is forced to rescue Archer at gunpoint.
Meanwhile, back at the office again, Malory is distraught to find that her office, too, was restored to its pre-FBI raid condition. The rest of the group continues touring the office, but Pam ducks into the Janitor's closet. Therein, she opens a secret passage to another new addition to the office; a Japanese-style hottub, undoubtedly meant to be kept a secret from Malory. Krieger is already inside, and still exhibiting faulty memories, assuming he even is Krieger and not a clone.
Back once again in Borneo, Archer and Kentaro relax after escaping the guerrillas. As they discuss their respective situations, Archer blacks out from a mix of pain medication and sake. He wakes up the next morning just in time to see Kentaro using his phone to find out about the bombings of Hiroshima and Nagasaki. Archer tries to console him, also to no avail, save a couple of broken ribs. Eventually, Kentaro decides to assist Archer on his mission in the hopes of catching a ride with him and returning to Japan. Having retrieved the objective for the mission, Archer prepares to blow the plane, but the guerrillas spot him. With Kentaro's help, the mission is completed and they make it to the extraction point relatively intact. Kentaro has second thoughts about leaving, but Archer, in an extremely unprecedented act of kindness, uses his phone to track down and call Kentaro's family, allowing him to talk to his wife for the first time in decades. When the CIA agents, tell them to hurry up Archer shoots the water in front of them yelling "Give us a minute!" as he watches Kentaro reconnect with his family.
Upon his return to the office, Archer is berated by Lana about his six week-long absence. Lana proposes some ground rules regarding Archer's role as a parent, and then leaves to feed Abbiejean. Before Archer follows, he reveals to Malory that he was in on the recreation of the old ISIS office and Milton, stating, "I'm not a huge fan of change."
- Title Explained: A "Holdout" is an act of resisting something or refusing to accept an offer. It can also refer to a person who does such an action. Here, this relates both to Kentaro's continuation of his duty despite World War II's conclusion and to Archer's hesitancy to take on his role as a father.
- "Cobra whiskey and lady-boy hookers" is a reference to Archer's semester abroad (presumably in college) that Malory mentions to Lana in Season 5's episode "House Call."
- While Archer is talking to Malory and Lana on the phone, he feeds a banana to a muntjac walking around his room. This is a subtle reference to the lady-boy hookers in the shower, and provides the answer to whether or not they are "genetic females".
- When Malory mentions smelling toast, that is reference back to Season 4's episode "Sea Tunt: Part 1," where Archer asks if she's having a stroke, and if she smells toast.
- The ISIS building's office has been remodeled back to its original state by Cheryl, Pam and Archer, seemingly out of spite knowing full well Malory wanted a more up-to-date renovation of the office.
- Pam is revealed to be back to her old overweight self while Cheryl has given up her identity as Cherlene and is back to her old self.
- Archer once again calls a Japanese person Kato as he did in "A Debt of Honor," referencing the sometimes-Japanese manservant/sidekick of the Green Hornet by the same name.
- It is revealed that Malory was the one who told Lana to use Archer's sperm in order to give birth to Abbiejean or A.J., although she denies it.
- Sato Kentaro may be a reference to real life Japanese war veteran Hiroo Onoda, who also remained on an island in the Philippines for 30 years after World War II.
- Archer notices that his situation in this episode mirrors that of a Six Million Dollar Man episode.
- Archer medicates himself with a concoction of candy and painkillers called "Mike and Vikes", named after the chewey candy Mike and Ikes.
- Brett's death in "White Elephant" is mentioned in this episode.
- Milton the Toaster, or simply Milton, was the original mascot for Kellogg's Pop Tarts during the 1970's. He was very popular with children during that time and had many products made after him.
- Ray's fan reads "売春宿," which means "brothel" in Japanese—a callback to Malory's accusation that Ray would have renovated the office in the style of a "Japanese whorehouse."
- Air America was a real CIA front company that posed as an airline.
- Tom Kane narrates the World War II-era news reels documenting Japan's defeat. He played a similar role at the start of every episode of Star Wars: The Clone Wars.
- The use of 934, 934TX, and 934TXS: When Pam does the retinal scan, the secret door unlocks and the code reads 934TXS.
- When Pam uses the retina scanner, her ID is "Shiro Kabocha", a reference to the name she used as a Yakuza drift racer.
- Lana: "So, why'd you run away when you were so excited about being a father when A.J. was born? Did reality set in?"
- Archer: "I... wait, was that rhetorical? Because the next time you decide to use somebody's sperm to impregnate yourself, then maybe that decision should include that other somebody!"
- Lana: "Who, that other somebody who runs away at the thought of responsibility and, as we speak, is up to his eyeballs in cobra whiskey and lady-boy hookers?"
- Archer: (with a bottle of cobra whiskey in hand) "Wh--that... that is... You don't know me!"
- Lana: "HA!"
- Lana: "And is this... is this Brett's blood?"
- Cheryl: "Ugh, no, just the same type. We had to fudge it a little on the stains. Some of which actually were fudge!"
- Pam: "And some of which merely resembled it."
- Pam: "Look, my therapist says everybody's got a hole that needs to be filled. Some people fill it with drugs, some fill it with work, some fill it with between-meal snacks and liquor and their therapist's cock!"
- Archer: "You're gonna need my help."
- Kentaro: "Heh, because you also need my help!"
- Archer: "Only because you just broke two of my ribs in addition to impaling me on a bamboo stake, on which I think we both know you smeared some poop!"
- Kentaro: "I..."
- Archer: "AND IF YOU DID, I DON'T WANNA KNOW!"
- Milton: [TOAST EJECTS]