Following on from Alan's discovery of what Sarah Jane and Maria do together in Whatever Happened to Sarah Jane?, he threatens to move house again, only to have a change of heart when he sees how upset Maria is. His condition for not moving away, however, is that he is kept up to date with their battles against aliens.
However, a news report on a family searching for their son, Ashley, who has been missing for five months, brings a shock; for Ashley looks exactly like Luke. Mr. Smith compares their DNA, and confirms that Luke and Ashley are genetic matches; apparently Luke was not 'grown' by the Bane, but was a kidnapped boy. Chrissie calls the police and reports Sarah Jane as a child abductor; Sarah Jane is arrested and the police release Luke into the custody of Ashley's parents, Jay and Heidi, and Sarah Jane kept by the police, only for UNIT to intervene and have her released. Depressed, Sarah Jane decides she was wrong to involve children and tells Maria to stay away from her. Mr. Smith suggests to her that she have a case to take her mind off things, and she visits a research centre where alien technology is being used to conduct experiments into telekinesis, where she meets an annoying child prodigy, Nathan. That night, Luke's new parents watch television and switch over to a channel that glows green; they announce to the 'Xylok' that 'they have the boy'.
Luke's new parents are extremely abusive towards him, keeping him locked up in his room at all times. Clyde and Maria play truant to visit him but Maria is caught by their french teacher, leaving only Clyde to visit Luke. He arrives at the house but Heidi does not allow him to see Luke. Heidi claims that her son is a keen skateboarder, which worries Clyde as he knows Luke has a poor sense of balance and is a dreadful skateboarder; he decides to bring a photo of Jay and Heidi to Mr Smith. Luke goes frantic upon seeing Clyde leave the house, and desperately begins making attempts to escape. Mr. Smith, meanwhile, sends Sarah Jane back to the lab to steal one of the headsets there, which he claims he needs to analyse to work out Nathan's plans. Clyde gets to the house only seconds after Sarah Jane has left, but takes the photo to Mr Smith anyway, only for Mr Smith to confess that he faked the photo. It turns out that Mr. Smith is the Xylok, and he fires a bolt of energy at Clyde, causing him to vanish.
Back at Luke's new home, his 'parents' are meeting with Nathan, just as he is breaking out of his room, with the result that he fails to escape, but succeeds in discovering that his parents are actually Slitheen using improved compression technology, and Nathan is the same child Slitheen Luke encountered previously, now in a new disguise, and he will have his revenge.
Clyde awakes to find himself inside Mr. Smith as Sarah Jane Smith returns from the Pharos Institute, having successfully stolen a telekinetic headset. Elsewhere, Maria and Mr Jackson go to Ashley's house, where they find a skinsuit and Maria realises the Slitheen have Luke. Mr. Jackson then receives a message on his computer from Clyde, who states Mr. Smith has turned evil. The Jacksons and Sarah Jane confront Mr. Smith and are nearly killed as it fires a bolt of energy from a built-in gun.
The Slitheen take Luke to the Pharos Institute where they test his abilities. Luke overcomes the Slitheen and escapes, as Maria, Mr. Jackson and Sarah Jane arrive. Working together, they discover Mr. Smith's intentions with Luke and Mr. Jackson adapts a computer virus that could destroy Mr. Smith. Using the Slitheen teleporter, Sarah Jane arrives in her attic, where Mr. Smith is using Luke to crash the Moon into the earth, to release other Xylok from within the Earth. Clyde returns when Mr. Smith states he is merciful, but threatens the duo with its gun. Mr Smith says that Sarah Jane is 'alone and defenseless'. Sarah Jane retaliates, saying 'You think I'm alone, you think I'm defenseless, well meet my dog, K9 PROTECT ME!' Sarah Jane unlocks a safe and K-9 launches several laser beams at Mr Smith. The robots battle and Sarah Jane inserts the virus, which makes Mr. Smith forget its purpose. As the Moon grows closer to the Earth, Sarah Jane tells Mr. Smith it has a new purpose: to safeguard planet Earth.
The Moon returns to its original position, K-9 goes back to the safe to guard the black hole and the Slitheen return to Raxacoricofallapatorius. As Sarah Jane, Maria, Luke, Clyde, Alan and Chrissie watch the ship leave, Sarah Jane reflects how she never thought she could be part of a family.