A news report on a family searching for their son, Ashley, who has been missing for five months, brings shock to Sarah Jane, for the missing boy Ashley looks exactly like Luke. Mr Smith compares their DNA, and confirms that Luke and Ashley are genetic matches, claiming Luke was not 'grown' by the Bane, but was kidnapped and experimented on.

Chrissie Jackson calls the police and reports Sarah Jane as a child abductor. Luke is released into the custody of his 'real' parents, Jay and Heidi Stafford, and Sarah Jane is arrested, only to be released by intervention of UNIT. Mr. Smith informs Sarah Jane that a research facility, called the Pharos Institute has been experimenting with psychic energy, engineered from alien tech. At the institute, she encounters a boy genius, named Nathan Goss, for whom she feels strangely uncaring.

Back at the Stafford's house, Luke is introduced to his room, and is suddenly locked inside by his 'parents'. Mr. and Mrs. Stafford turn on their television and report to a being they call "the Xylok", saying that they have captured Luke.

The Slitheen are back for revenge, having used advanced compression tech to hide inside the skins of the very skinny Stafford couple and Nathan Goss.

The Xylok, mastermind of the scheme, turns out to be the alien computer Sarah Jane knows as Mr. Smith, carrying out the master directive given him by his original creators.
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!!Tropes

* AIIsACrapshoot: Mr. Smith is the Xylok, and he's evil. Although strictly speaking he's working exactly as his original designers intended him to, [[EvilFeelsGood albeit with a certain relish.]]
* AmnesiacVillainJoinsTheHeroes: This happens to Mr. Smith at the serial's end. Sarah Jane wiping his memories with a computer virus causes him to forget his original nefarious purpose and forces him to latch onto the first purpose Sarah Jane gives him -- saving the Earth -- before he fully shuts down. As explained by Sarah Jane at the end and demonstrated in later episodes, Mr. Smith will reboot from his shutdown, but he'll have a new purpose as Earth's defender; this time ''for real''.
* ApocalypseHow: Mr. Smith attempts to create a ApocalypseHow/Class4 to ApocalypseHow/ClassX by telekinetically ''dragging the moon out of its orbit and crashing it into the Earth''.
* BatmanGambit: The Xylok's plan. He didn't expect the two parties being manipulated to join forces against him.
* TheChessmaster: The Xylok.
* DeathOfAChild: Implied but not shown; Korst, the young Slitheen, is wearing a twelve-year-old boy disguise that (given what is revealed about Slitheen disguises in their first ''Doctor Who'' appearance) must have been made by killing and skinning a real twelve-year-old boy.
* DramaticDrop: Maria drops the plate she's holding when she sees a news report about a missing boy who looks exactly like Luke.
* EvilAllAlong: Mr. Smith. Although the heroes at first suspect a ComputerVirus or something else has caused Mr. Smith to go through a FaceHeelTurn, it's revealed that Mr. Smith has always been this and was waiting for the chance to make his move. In a rather interesting play on this trope, Mr. Smith remains a part of the main cast after this episode and everything goes back to normal as a result of the heroes enforcing AmnesiacVillainJoinsTheHeroes on him.
* ExposedExtraterrestrials: Slitheen, when not in human suits.
* FunWithAcronyms: MITRE.
* INeverSaidItWasPoison: Luke realises something's amiss when his fake father mentions Maria and Clyde's names despite never meeting them.
* IdiotBall: The Slitheen impersonating Luke's father leaves his human skinsuit behind at the house for no better reason than so Maria can find it later and realise the Staffords aren't really Luke's parents.
* InsufferableGenius: Nathan Goss.
* KilledOffscreen: The real Staffords and Nathan Goss were both killed some time before the events of this story. (The novelisation adds a prologue which reveals the Staffords were really Nathan's parents, Marco and June Goss.)
* LaserGuidedAmnesia: What Alan does to Mr. Smith, making him into a good guy.
* LaserHallway: The Pharos Institute has a dramatic but impractical ''outdoor'' laser grid. Which, even apart from the fact that Sarah Jane just zaps it with her sonic lipstick, completely fails to make up for the fact that there's apparently no security systems installed ''inside''.
** To their credit, if it was anybody ''other'' than Sarah Jane, The Doctor or one of his companions, it would probably fry them alive. If it didn't, the ''security guards on Motorbikes'' probably would.
* NaturalDisasterCascade: Provider of the trope image. When [[spoiler:[[EvilAllAlong Mr. Smith]]]] forces [[spoiler:Luke]] to telekinetically pull the moon towards Earth on a collision course that will shatter the Earth, the gravitational disturbance from the moon moving causes spontaneous freak natural disasters which begin tearing apart the planet. Sarah Jane states this will kill all human life on the planet long before the moon makes impact.
* NoEndorHolocaust: Averted. When the Moon was being pulled towards Earth, the fact that these events caused disruption such as freak storms, harsh weather, and complete collapse of the environment is mentioned through the scattered news reports and footage which Sarah Jane was watching so it wasn't glossed over.
* ReadingsAreOffTheScale: Luke's psychic energy.
* ScrewTheRulesIHaveConnections: UNIT don't abandon their own and pull strings to get Sarah Jane off on child kidnapping charges. Of course she's actually innocent; they would likely be less understanding otherwise.
* SealedEvilInACan: The race of supercomputers that Mr. Smith belongs to.
* SeasonFinale: A larger-than-normal set of stakes, returning villains, and a few revelations with the potential to seriously upset the status quo.
* SmarterThanYouLook: Mr. Smith [[VillainRespect complements]] Clyde’s intuitive way of warning his friends about the situation, despite being trapped on a different plane of existence; he notes how Clyde is [[HiddenDepths smarter than he usually lets people see]].
* SpotTheThread: Clyde realises something is amiss when a) Luke’s “mother” looks nothing like him and b) she claims that “Ashley” was stunning on a skateboard, when Clyde has seen Luke on a skateboard and knows how terrible he is.
* TheTrapParents: Luke is reclaimed by his real parents, and forced to say goodbye to his friends in Bannerman Road. It turns out that they're not his real parents, but part of a hostile alien scheme.
* WasOnceAMan: We're led to believe Luke isn't an alien created ArtificialHuman after all, but had been a normal human boy experimented on and kidnapped from his family, and thus unwittingly kidnapped by Sarah Jane.
* WhamEpisode
* WhamLine:
--> '''Clyde:''' I've got this. It's a picture of Luke with that pair that reckon he's their kid. Only I think it's a fake, see? I thought you could do your analysing thing and-\\
'''Mr. Smith:''' You're right, Clyde. It is fake. [[TheDogWasTheMastermind I faked it.]]
* YouKilledMyFather: Korst, the young Slitheen boy from ''[[Recap/TheSarahJaneAdventuresS1E1E2RevengeOfTheSlitheen Revenge of the Slitheen]]'' disguised himself as Nathan Goss, and wanted to drain Luke of all his psychic energy, as revenge for his father, Kist being killed by his own machinery, although he didn't realise that Sarah Jane actually tried to save them both.
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