The film opens in a California forest as a group of alien botanists collect flora samples. U.S. government agents appear on the scene, and the aliens flee in their spaceship, mistakenly leaving one of their own behind. The scene shifts to a suburban home, where a 10-year-old boy named Elliott is trying to hang out with his 16-year-old brother Michael and his friends. As he returns from picking up a pizza, Elliott discovers that something is hiding in their tool shed. The creature promptly flees upon being discovered. Despite his family's disbelief, Elliott lures the alien from the forest to his bedroom using a trail of Reese's Pieces candy. Before he goes to sleep, Elliott realizes the alien is imitating his movements.Elliott feigns illness the next morning to stay home from school and play with the alien. Later that day, Michael and their five-year-old sister Gertie meet the alien. They decide to keep him hidden from their mother. When they ask it about its origin, the alien levitates several balls to represent its solar system and then demonstrates its powers by reviving a dead flower plant. But after the balls fall down to the ground, Elliott realizies that the Government are searching for the alien.At school the next day, Elliott begins to experience a psychic connection with the alien, including exhibiting signs of intoxication due to the alien drinking beer, and he begins freeing all the frogs in a biology class. As the alien watches John Wayne kiss Maureen O'Hara in The Quiet Man, Elliott kisses a girl he likes.The alien learns to speak English by repeating what Gertie says as she watches Sesame Street and, at Elliott's urging, dubs itself "E.T." E.T. reads a comic strip where Buck Rogers, stranded, calls for help by building a makeshift communication device, and is inspired to try it himself. He gets Elliott's help in building a device to "phone home" by using a Speak & Spell toy. Michael notices that E.T.'s health is declining and that Elliott is referring to himself as "we".On Halloween, Michael and Elliott dress E.T. as a ghost so they can sneak him out of the house. Elliott and E.T. ride a bicycle to the forest, where E.T. makes a successful call home. Meanwhile, the Government secretly head to Elliott's house and his room. The next morning, Elliott wakes up in the field, only to find E.T. gone, so he returns home to his distressed family. Michael searches for and finds E.T. dying in a ditch and takes him to Elliott, who is also dying. Mary becomes frightened when she discovers her son's illness and the dying alien, just as government agents invade the house.Scientists set up a medical facility there, quarantining Elliott and E.T. Their link disappears and E.T. then appears to die while Elliott recovers. A grief-stricken Elliott is left alone with the motionless alien when he notices a dead flower, the plant E.T. had previously revived, coming back to life. E.T. reanimates and reveals that his people are returning. Elliott and Michael steal a van that E.T. had been loaded into and a chase ensues, with Michael's friends joining them as they attempt to evade the authorities by bicycle. Suddenly facing a dead end, with people with guns, Elliott closes his eyes preparing for death. They escape as E.T. uses telekinesis to lift them into the air and toward the forest.Standing near the spaceship, E.T.'s heart glows as he prepares to return home. Mary, Gertie, and "Keys", a government agent, show up. E.T. says goodbye to Michael and Gertie, as Gertie presents E.T. with the flower that he had revived. Before entering the spaceship, E.T. tells Elliott "I'll be right here", pointing his glowing finger to Elliott's forehead. He then picks up the flower Gertie gave him, walks into the spaceship, and takes off, leaving a rainbow in the sky as Elliott (and the rest of them) watches the ship leave.
- Littlefoot and the Land Before gang, Thomas the tank engine, Percy, James, Toby, Emily, Gordon, Henry, Edward, The Logging Locos (Bash, Dash and Ferdinand), Luke, Hiro, Charlie, Paxton, Victor, Kevin, Stanley, Rosie, Twilight Sparkle, Pinkie Pie, Rarity, Applejack, Rainbow Dash, Fluttershy, Spike, The Cutie Mark Crusaders (Apple Bloom, Sweetie Belle and Scootaloo), Shining Armor, Princess Cadence, Heckle and Jeckle, Sophie, Sky, Cool McCool, Bloom, Kids World's Adventures Team and the characters will guest star in this film.