While secretly investigating Clark, Lana finds herself being stalked. The stalker calls Lana and threatens to kill her. She takes refuge in Clark's house, seizing the opportunity to search for things that can unravel Clark's mystery.

The stalker turns out to be one of Lex's guards; he dies from falling off a roof when trying to kill Lana. Of course, Lana can't be dead, and she is saved again by Clark.

Chris falls in love with Anna, an intern at the vet office. Their relationship is jeopardized when he belittles her on Peter's advice.

Peter steals a parrot and shows off in front of his friends. Inspired by Joe, Peter decides to become a pirate. During a robbery, the parrot is injured and died shortly after.

Chris is distraught after Anna breaks up with him. Lois comforts him, encouraging him to apologize to Anna, and he does. Anna forgives him and they are reconciled.

Having applied a special lipstick to her mouth, Lois develops an infatuation with Clark under the influence of red Kryptonite, which is used as an ingredient in the lipstick.
Clark is immediately infected when kissing Lois, and starts losing his mind. After wrecking havoc at Lex's engagement party, he takes Lana to his barn. Lex confronts Clark with a gun. Martha is able to neutralize the effect with green Kryptonite before someone gets hurt.

Brian pays a visit to his former girlfriend Tracy, and he is shocked to discover that they have a son, Dylan, who is already a teenager.
Brian is disappointed at Dylan's uncivilized behavior and resolves to guide him on a right path. He bonds with his son under the influence of marijuana, and soon becomes overprotective.

Clark is attacked by a phantom zoner in the barn; he is experiencing an alternative reality created by the zoner.
In the hallucination: he is held in an asylum, having no power, and is told that all his memories are fabricated by himself to avoid reality after his parents died in the meteor shower; Lana is still in love with him; Lex is a paraplegic; his mother is married to Lionel. To cure his disease, he has to undergo a operation.

But he finally snaps out of it with the help of a mysterious man previously saved him from another phamtom escapee.

Peter constantly hangs out with his friends, ignoring Lois.
Brian has won a reward for his essay and invites
Peter and Lois to the awarding ceremony. Peter is unable to stay sober after arriving at the hotel, so Brian takes Lois out to have fun. That night, Brian sexually harasses Lois while they are watching a movie. A fight ensues after Peter accuses Brian of his inappropriate act.
Brian apologizes to Lois, who forgives him.

While Peter and Lois are on vacation, Herbert is enlisted to babysit the children. Chris eventually suspects that Herbert is a pedophile.

Bart returns to Smallville, and he is captured while sneaking into one of Lex's facility to get information about 33.1.
Victor and A.C. are now working with Oliver, with Clark and Chloe's help, they orchestrate a plan to rescue Bart. The plan has succeeded, and they blow up the facility before striding out.

Peter lost his wallet during a Barry Manilow concert. His Visa bill reveals that his credit card has been compromised. Brian accompanies Peter to a chinese restaurant where the credit card has been used several times. Although the place is packed, Brian manages to locate the wallet, but before they can reach for it, James Woods appears in front of them, taking the wallet away. Peter is forced to leave his house after James blatantly steals Peter's identity. Living in a shabby hotel, Peter and Brian plan to get back at James. At a TV show, Peter convinces the host that he is James Woods with the paperwork forged by Stewie; he recklessly mocks 9/11 and completely ruins James' reputation .
James confronts Peter in a bar, but just like the first time, Peter and Brian use candy bars to tempt him into a crate.

Lois suspect that Oliver is the Green Arrow and sets a trap for him. Clark helps Oliver out by dressing up as the Green Arrow. Linda Lake - a columnist of The Daily Planet and a victim of the meteor rock, possessing the ability of morphing into water - uses her ability to violate other people's privacy in order to come up with interesting story. While searching through Linda's computer, Chloe finds a article about Clark's alien lineage; Linda appears from behind, and they engage in a fight. Linda is defeated and hit by Lana' SUV. Lana talks to Clark and wants to reconcile with him. But given the fact that Lana is carrying Lex's baby, Clark turns her down, prompting Lana to accept Lex's proposal.

Peter has developed an obsession with mustache. While trying to save a man from the burning McBurgertown, he burns his mustache to a cinder. The man Peter saved turns out to be the manager of McBurgertown; to show his appreciation, he offer Peter lifetime supply of burgers. At McBurgertown, While eating the 30th burger, Peter suffers a stroke. After being hostipalized, he is frustrated to learn that the left part of his body is paralyzed, and he blames McBurgertown for his misery. Three months later, Peter passes by a Stem Cell Research Lab; he limps in and five minutes later, walking out completely healed.
Peter and Brian disguise as investors and infiltrate McBurgertown's headquarter to find criminal evidence to damage its reputation.
They find a slaughterhouse in the building, and a talking cow, which is willing to testify against the company.
Brian wagers that Stewie can't become the most popular boy in highschool. But he is wrong, and not only does Stewie become the most popular boy, he also gets a date with Connie D'Amico, who breaks up with Stewie because of his "baby penis".

Jed Mcnally exploits illegal immigrant labor and bury those who tries to escape underground. Javier escaped from Mcnally's farm, and Clark takes him in.
Clark exposes Mcnally's crime and get him arrested, but he escapes and burrow into the ground.
With Chloe's help, Javier reunites with his mother.
Mcnally is captured by Lex and imprisoned in the 33.1 laboratory.

Quahog is struck by a flash flood, which overwhelms the first floor of the Griffin's house. While trying to retrieve a case of beer from the fridge, Meg drowns after her shirt gets stuck.
At the hospital, Peter is regretful for what he had done to her and vows to treat her like a princess once she recovers. Meg falls in love with Michael, the doctor she met when she wakes up.
Disguising as a Chinaman, Peter spies on Meg when she is dating Michael. Michael recognizes him and breaks up with Meg.
Two weeks later, Meg finds herself pregnant. Peter takes Meg to Michael's house to confront him. To their surprise, Michael proposes to her upon hearing the news.
At the wedding, Meg realizes that she isn't pregnant and tells Michael the truth, prompting
him to bail out immediately without saying a word.

Brian and Stewie invest in a dilapidated house, but fail to fix it up. The house explodes in an accident. They are broke.

Peter discovers that he is a Mexican immigrant and loses his job at the brewery. Lois' father offers Peter a job at his manor, where he empathizes the other immigrant and they become friends. After being treated unfairly, Peter rallies his coworkers to confront Mr.
Pewterschmidt, who offers Peter American citizenship to quell the commotion.

Stewie escapes when Lois recounts what happened after she fell into the ocean. Back at the Griffin's house, he holds his family hostage and points a gun at Brian forcing Brian to drive him to the CIA headquarter after tying up the rest of his family. Having taking control of the world's power grid, he becomes the president of the world.

After Chris sets his family free, they find a secret chamber in Stewie's room. Lois gets fed up with Stewie's tyranny; she arms herself with a knife and some heavy weapons before proceeding to kill her baby.

In a fierce fight, Lois subdues Stewie, but can't kill him. When Stewie is about to kill Lois, Peter arrives, shooting Stewie in the head.
It's then reveals that the whole story is just a simulation. None of them was really happened.