Plot:
The film opens with Scorch Supernova (Brendan Fraser) on a mission to rescue captured babies from the Gnarlachs. He rescues them just in time before the Gnarlachs wakes up. Scorch then returns to Planet Baab where he is known as a famous hero and a love interest for anchorwoman Gabby Babblebrook (Sofía Vergara) while at BASA his brother Gary (Rob Corddry) works. Gary's son Kip (Jonathan Morgan Heit) is a big fan of his uncle Scorch. Soon, Gary and Scorch receive a message from Lena Thackleman (Jessica Alba), the head of BASA, that Scorch will be sent to the "Dark Planet" (Earth) due to an SOS call. Scorch decides to go on the mission to the Dark Planet, but Gary strongly insists that he doesn't go because he is not serious. Also, no alien has ever returned from the dark planet. After further arguing, Gary finally says that he won't be helping Scorch and quits BASA before Scorch himself fires him. Gary then goes home to his wife Kira (Sarah Jessica Parker) and Kip only to find out that Scorch has already gone on the mission to the Dark Planet, while Kip is watching it on live TV in excitement.
Scorch arrives on Earth and lands in the desert and finds a 7-Eleven convenience store but mistakes an airdancer for a dying being. Scorch is then tranquilized and captured by General Shanker Saunderson (William Shatner), the malevolent general of the US Army, and is taken to "Area 51" where aliens from other planets are held. After finding that this has happened, Kip wants to go rescue Scorch but Gary discourages him and he himself doesn't want to go. Kip is angry and goes to his room. Gary goes to Kip's room to apologize and admit that he is sorry about Scorch. When Gary flips Kip's blanket open, instead of seeing Kip, he sees his dog and that Kip's window is open. Knowing that Kip is going to try and save Scorch, he rushes to BASA with Kira wearing his rocket boots. They arrive to find that Kip is about to take off in a ship.
Gary manages to cancel the launch sequence, but he re-activates the sequence so Gary himself can rescue Scorch. He soon arrives on the Dark Planet. As soon as he arrives his ship immediately activates a self-destruct sequence, but Gary manages to get out. He then arrives at the same store that Scorch arrived at earlier. Gary goes inside there, but is spotted by two men inside named Hawk (Steve Zahn) and Hammer (Chris Parnell). Both Gary and the two men get freaked out by each other and try to hide from each other. After the two men realize that Gary is not a hostile alien, they offer him a Slurpee. Gary takes it but drinks it too fast and gets brain freeze. Afterwards, Shanker's men break into the store and capture Gary, taking him to Area 51.
Gary is then taken to Shanker's office where he is quickly removed after Shanker receives an incoming call. It is then revealed that Lena is an ally of Shanker's as she has sent him a powerful source known as blubonium and is in love with him as he puts on an Elvis Presley-like wig when contacting her. Gary is placed in a cell hall with other alien geniuses named Doc (Craig Robinson), Io (Jane Lynch), and Thurman (George Lopez), who tell Gary that various human technology has been invented by them for Shanker to rip off and sell to the world so he will release them from Area 51. With these technologies made by the aliens, Shanker had made deals with companies like Apple Inc., Facebook, and Google to distribute the technologies to them. Gary reunites with his brother, but is again annoyed by his conceited behavior. After a food fight in the cafeteria, the aliens make their way to 'the peace shield'. Meanwhile, Lena captures Kira, who stayed at BASA to try to contact Gary in concern for his safety. Lena then reveals her plan to give a lifetime supply of blubonium to Shanker.
After Shanker reveals the blutonium, Gary unintentionally provokes Scorch into stealing it after stating its dangerous power and when being chased, Scorch destroys the blutonium, causing Shanker to freeze him. He orders Gary to fix the blutonium and reveals that he's going to destroy all of the alien planets with a laser ray using the blutonium. Shanker says that all aliens are hostile just because a grey alien spaceship killed his dad in 1947. Gary fixes the ray with help from his new friends, but Shanker goes back on his promise to release him and instead freezes him like his brother. The other aliens discover Shanker's true intentions when he tries to destroy Baab with the laser ray and mutiny, knocking out Shanker's henchmen. However, it is revealed that Gary did not put the machine together fully and it malfunctions, destroying itself before it can destroy Baab. With Gary and Scorch released from their icy prisons by the machine alongside the other frozen aliens, the brothers, Doc, Thurman, and Io escape Area 51 and eventually find Scorch's ship in a trailer park. With help from Hawk and Hammer (who live together in the park), Gary and his friends get into the spaceship and take off after helping to narrow its location down with a tornado scare.
Meanwhile, back on Baab, Kip frees his mother, who stops and subdues Lena after the latter took off with the blutonium shipment (and in the midst of the battle, learns Shanker was using her). US Air Force jets chases Gary's saucer, but Kip guides his father through and manages to destroy the jets by making the spaceship pull up suddenly over a waterfall while the jets ram into it. However, Shanker (wearing Scorch's robotic suit that he wears on his adventures) uses a tractor beam to stop the ship, and freeze it in midair. Gary and Scorch jumps on and manages to get the suit off from Shanker which causes him to fall to his death. Suddenly, Scorch and Gary begin to plummet to their dooms but they and Shanker are rescued by the captured grey aliens (the ones who accidentally killed Shanker's dad) who have their own plans to deal with Shanker.
Scorch, Gary, Doc, Thurman, and Io return to Planet Baab, where Gary is reunited with his family. Scorch is greeted as a hero, but gives the credit to his brother which the citizens of Baab celebrate. Scorch then embarks on his toughest mission yet: marrying Gabby Babblebrook. Hawk and Hammer are also present at the wedding as the inflatable wavy arm figure is also patched up.