Shaquille O'Neal and Dr. Phil wake up to find themselves chained to pipes in a bathroom. Their host, Billy the Puppet, reveals that the room is slowly filling with nerve gas with the only way out being to make a basket and get the saws, which have to be used on their feet. Unfortunately, Dr. Phil saws the wrong foot and faints, leaving the two to die.
In New York the recently widowed Cindy Campbell (Anna Faris) visits her brother-in-law, Tom Logan (Charlie Sheen), inquiring about her loneliness with the departure of her nephew, Cody, to the army. Tom's attempted suicide results in his ingesting viagra, which greatly swells his penis and causes his death when he falls off the railing. Afterwards, Cindy takes a job to care for Mrs. Norris (Cloris Leachman), who lives in a haunted house. Next door is Tom Ryan (Craig Bierko), who runs into Mahalik (Anthony Anderson) and CJ (Kevin Hart), learning about their homosexual one-night stand. He is greeted at home by the arrival of his estranged children, Robbie (Beau Mirchoff) and Rachel (Conchita Campbell). Tom and Cindy bond over the following day, Cindy confiding to him about her husband, George's (Simon Rex) death in a fateful boxing match. The two realize their newfound love, but are interrupted by a gigantic triPod which disables electricity and starts vaporizing the town residents.
Cindy converses in mock Japanese with the haunted house's ghost, Toshio (Garrett Masuda), learning that the answer of the invasion is his father's heart. While Tom leaves the city with his children, Cindy reunites with her friend, Brenda Meeks (Regina Hall), miraculously alive after her death. Following Toshio's directions, the two head to the countryside and end up in a mysterious, isolated community. They are captured and put to trial headed by Henry Hale (Bill Pullman). The result allows them to live but never leave the village. Meanwhile, an emergency United Nations meeting, headed by the eccentric U.S. President Baxter Harris (Leslie Nielsen), who is reluctant to stop reading "My Pet Duck", goes awry when a weapon scavenged from the aliens renders everyone stark-naked.
Tom and his children drive and find themselves in the middle of a war between the U.S. military and the aliens. Excited with the conflict, Robbie runs away, while Tom and Rachel are taken by the triPod. Back at the village, Henry is killed by the village loon, Ezekiel (Chris Elliott), revealing to Cindy that he fathered Toshio, who was killed during Cindy's boxing match. Cindy and Brenda are soon taken by the triPod and sent to the bathroom seen in the prologue. Cindy manages to get through Billy's challenge, but is threatened with the safety of Tom and his children, who are put to traps. Looking at a toilet with the "heart" nearby, Cindy realizes that Billy, through Henry's wife, is the true father of Toshio. Seeing how far Tom would save his children, Billy apologizes for the invasion and releases them. Robbie and Rachel are successfully returned to their mother (Molly Shannon), who is revealed to have married a much older man. Brenda also becomes acquainted with Billy's friend, Zoltar.
An epilogue set nine months afterward, narrated by James Earl Jones who is subsequently hit by a car, reveals Brenda's giving birth to her child with Zoltar, Mahalik and CJ resuming their relationship, and President Harris being contented with his duck. Meanwhile, Tom appears in The Oprah Winfrey Show and wildly professes his love for Cindy by jumping around, throwing Cindy, and crushing Oprah's wrists.
They were captured and put to trial headed by whom?
Henry Hale