Stan is humiliated at work when a new agent, Duper, bests him in an operation simulation. He grows even more bitter when the new guy takes over his more prestigious assignments.
When Stan complains about this at home, Francine suggests that they invite his boss, Deputy Director Bullock to dinner, and some bootlicking. Because of that, however, Roger will have to hide in the attic all night. The alien complies, but when he finds himself out of a drink while watching his favorite show, Dynasty, he goes downstairs to get a refill. Meanwhile, Stan's dinner with his boss is going very well, until he sees Roger walk by the kitchen door. Stan makes an excuse, goes in the kitchen and pushes Roger into the bathroom, going in himself to scold Roger some more. When Bullock knocks on the door asking to come in to discuss Stan's promotion, Stan freaks and tries to get Roger to hide in the bathtub. This causes the Alien to get nervous and start gushing his ooze all over the bathroom. When Bullock forces his way in, Roger is already hidden, but the bathroom is filthy, and this costs Stan his promotion.
After Bullock leaves, Stan reprimands Roger on his behavior, which only causes the alien to get even more stressed, and gush more ooze in the dining room. When Stan finally tells him that the family would be better off without him, Roger feels sick and falls down, seemingly dead. Stan thinks he's just being a drama queen, and tells everybody to ignore him and go to bed. In the next morning, however, as Roger is still lying there, with flies hovering over him, Stan confirms that he is dead. He promises the family to give Roger's body a fitting funeral, but then throws it in a dumpster by a drive-through restaurant. Steve, who is extremely disappointed in Stan for his behavior, decides that he needs a new father figure, and ends up with Klaus as one.
Later, Roger later wakes up in a landfill, and it is revealed that he had gone through a stress-induced hibernation. Desperate, Roger finally figures that he can go back home disguised as an old lady. While on his way, however, he gets confused with one of the senior citizens who are on their way for a tour in Washington D.C., and gets shoved into a shuttle. In it, Roger befriends an old lady named Gertie who sympathizes with his family troubles. When in Washington, Roger visits the Oval Office, and decides to get hammered in it with his newfound friend. While drinking away, Roger's hat falls off and his alien image is captured by a camera of the internal security system.
Meanwhile, following Roger's death, Francine tries to get her priest to say a word for Roger, her "pet" in next Sunday's service. To her dismay, the priest informs her that only human beings, as well as apes capable of sign language, are allowed into Heaven, where as Roger will go to Hell. Francine is extremely disappointed in a God who would not let Roger into Heaven, and loses her faith. She then begins teaching her bible classes the truth about body decomposition. Stan, on the other hand, starts dealing with his feelings of missing Roger. He goes to a psychologist, where he reminisces his first encounter with Roger: the alien had escaped containment in Area 51 and was running around the base looking for cover. Stan joined the pursuit squad and eventually cornered Roger in a lab where theremin music was coming from. Roger pleads mercy, saying he means no harm. Stan is perplexed at Roger, for he was told that he'd be bigger and with claws. Roger shows he has claws by insulting on how fat Stan is. Immediately after, the squad also locates the alien and floods the room with hand grenades. Stan tries to lead Roger out of there and turn him in, he bumped his head into a lamp and was knocked unconscious. Roger managed drags Stan out, throwing Stan and himself into the laundry chute just before the grenades explode. The two end up in a laundry transport truck going out of the base. When Stan comes to, he realized that the alien had saved his life and offers repayment. Thus, it is revealed how it was that Roger saved Stan's life in Area 51 and came to live with the family. As it turns out, however, the psychologist was working for the CIA, and all of Stan's colleagues were watching his session in secret. Stan is now seen as some "weak link" in the agency, a "lady" because he shed a tear when reminiscing about that time.
When joining his team in the briefing room, Stan sees the footage from the White House that shows Roger. Bullock reveals then that they are certain that this is the alien that escaped from Area 51 four years ago, and orders him apprehended, so that they can also punish horribly whoever it was that harbored the alien for all that time. At every horrible sentence, Stan spits hot coffee that only his mouth could handle on his unsuspecting co-workers. In order to save his own butt, literally, Stan runs out, determined to find Roger before the CIA does and bring him home. As he is driving, however, he receives a call from a drunk Roger, who is calling from a pay phone in Washington to tell Stan off for dumping him in the garbage. When informed by Stan that the CIA is after him, he threatens to rat Stan and his family as the ones who harbored him. After hearing that, Stan decides that the only thing left to do to ensure his family's safety is to kill Roger before the CIA can get to him. He searches all over town until he sees two women slapping each other. It reminds him of Dynasty.
Roger continues his tour of Washington with Gertie, but he is shocked to find out that his new friend is actually a raging bigot, who hates Abraham Lincoln for having freed the slaves. He calls Hayley at home, asking the family to come pick him up. Hayley drag Steve and Francine with her, without telling the actual reason for the trip. They finally find Roger at the Smithsonian, where a Dynasty exhibit was being held and upon seeing him alive, Francine's faith is restored, since she believes that a miracle has happened. Immediately after, however, Stan arrives, knowing that Roger couldn't resist a federally funded Dynasty exhibit and he starts shooting at Roger while pursuing him across the museum. He finally corners the alien in a small room, but his family gets in the way, not willing to allow Roger to be executed. Then, the CIA, led by Bullock himself, knocks at the door, demanding that the alien surrender himself. When Roger shows a disposition to turn himself in and be killed by Stan in order to save "his family", Stan changes his mind and decides that he must save Roger. He then has an idea: he strips and de-wigs Gertie and turns her in as the alien. Bullock buys it and takes the "alien" in, promising Stan his old status back for the apprehension. He scratches the "too incompetent" off Stan's record and replaced it with "lady" and "not a".
At home, Francine asks Roger how Heaven was. Roger doesn't know what she was talking about until Hayley kicks him, causing him to fake the whole thing. Francine now believes that God works in mysterious ways.