It's the first day back at school after the holidays and the giant doll still stands in the school grounds as a reminder of the events which occurred at Sandy Bay School last term. A re-geniused Elizabeth shrinks the giant doll and interrupts the new principal at assembly so she can wipe everyone's memory. Her plan succeeds except for Toby and Russ, who escape with their memories in tact. New boy in town, Jack Bailey, sees the shrink ray in action and is determined to find out what's going on.
Charming, manipulative new student Jack befriends Garth so he can gather information about the shrink ray which he saw Garth use to shrink the giant doll. Garth is initially so impressed by Jack's friendly overtures he rebels against Elizabeth - but not for long. Elizabeth, distraught when Sacha beats her by one percent on a science assignment, seeks revenge and invents a 'Dream Catcher'.
Toby has his eye fixed firmly on Jack's sister Nikki. He is desperate to impress her, but how? Given she's a swimming star, he decides his best chance is to get on the school swim team. There's only one problem - Toby's a pathetic swimmer! Toby uses wicked science to invent a body oil to help move through the water like a seal. This threatens Garth's tenuous position on the swim team and when Elizabeth learns what Toby's up to she intervenes, tampering with Toby's oil.
Elizabeth catches a bad cold from Verity. With a raging temperature, her power to hyperfunction and use her genius is out of control. She finds herself acting against her will, fulfilling other peoples' wishes - a cold cream for Verity, sunglasses which give Russ scientific formulae and an exo-skeleton for Garth, transforming him into an armoured warrior Garthdor. The illness worsens and Elizabeth, close to death, calls for the only person who can save her - Toby.
Trying to help his friend, Russ finds himself forced to masquerade as Toby at a meeting with Nikki in the surf café. Wearing a Toby invention - a hi-tech polymer vivo interface suit (which makes Russ look and sound exactly like Toby), Russ might look like Toby but he's still Russ and clumsy. He knocks the suit's controls resulting in a malfunction, causing Russ to chaotically transform into multiple identities in the middle of the Surf Cafe.
When Russ is bullied by Garth, Toby tries to prove Russ is not a loser. Toby creates a time portal to show Russ his ancient, valiant ancestors. But things go horribly wrong. The time machine is damaged and Russ finds that he's swapped places with his 350,000-year-old hominid ancestor, Rog. While the caveman battles with Garth at a twenty-first century school, Russ is hailed as leader of a tribe of cave-dwelling hunter-gatherers.
Disaster strikes when the school clock breaks and Elizabeth is forced to hide her lab equipment in the school storeroom or risk Mr Woods discovering her secret laboratory. A curious Jack accidentally locks himself in the storeroom and is zapped by one of Elizabeth's new inventions, causing his arm to go right through the door. Now Jack has direct and very personal experience of Wicked Science, but has no idea how dangerous it is as he begins to disappear.
Flagging morale and shocking times have hurt the Sandy Bay swim team. Nikki is suffering most of all so, in order to boost her confidence, Toby invents a 'doubt eliminator' in the form of a ring. But the device falls into Verity's hands, and with an unbounded faith in her own abilities, she starts a cheerleading squad and asserts her independence from Elizabeth.
Sacha has been feeling increasingly homesick over the last few weeks and misses her horse, Misty, terribly. Feeling sorry for her, Toby invents a homing device that teleports her horse to Sandy Bay. But the device malfunctions and Misty keeps appearing next to Sacha in school. Meanwhile, Elizabeth is desperate to prove to Toby that they are meant to be together and she lures him into a Wild West virtual reality world.
Russ continues to be on Toby's back about helping him with girls so Toby invents a flying disk to make Russ look good on the beach. That tactic fails, of course, but Jack is convinced the flying disk is another example of Toby's weird powers. He encourages Nikki to go on a date with Toby - even helping him by setting up a romantic lunch for two at the café. Elizabeth's jealousy is piqued and she invents a chameleon gel to make herself invisible.
A hungry Garth is a careless Garth and when he "borrows" Elizabeth's shrink ray to increase the size of his breakfast, Jack not only sees the device in action, but steals it. Chaos results when Jack unwittingly uses the shrink ray in reverse on a koala.
The 'sibling' rivalry between Sacha and Russ escalates to the point where the trio threatens to break up. During a heated argument, they manage to trigger some of Toby's wicked science devices and as a result find they have swapped bodies. Now Russ is in Sacha's body and Sacha is in Russ'. They find themselves on a very sharp learning curve as each discovers what life is like for the other.
Elizabeth is driven wild with jealousy when Toby and Nikki decide to go to the school dance together. She invents a lightning generator, producing a fork of pure lightning which pursues Nikki. In fact, it does a right-hand turn frightening Nikki so much that Elizabeth is able to blackmail Toby into taking her to the dance. An unlikely pairing of Russ and hockey player Peta provides comic relief, but Jack manages to steal the lightning controller from Verity.
Toby's liquid nitrogen cryogenic refrigeration chamber malfunctions, spelling potential disaster. The Raptor cells stored inside begin to thaw and Toby must allow them to grow or lose them. Meanwhile, Jack is eager to learn more about Toby. He orchestrates events so Russ, Toby and Sacha are all distracted, allowing him the opportunity to raid the bungalow.
Working on the odd theory that if she makes Toby desperately ill, he will come running to her for a cure, Elizabeth invents a device that drains his hyperfunctions. To get his sympathy she pretends that she is suffering too. But the device has an unexpected side effect when Sacha is inadvertently zapped and awakes to find that she can communicate with animals.
After damaging an experiment involving a rare plant from Boggy Creek, Verity is banished from Elizabeth's lab. To her horror, she starts growing scales and gradually turns into an amphibious monster! As rumours of the strange creature spread, Verity is delighted to find she can terrorize Garth and decides to pay out on him. Knowing an oblivious Garth and Elizabeth are returning to Boggy Creek for more samples, Sacha realises Garth could be in real danger.
Jack films the lead-up to an inter-school Science Expo as an excuse to find wicked science and hopefully blackmail Elizabeth and Toby into making him a genius too. When Elizabeth hears Sacha's exhibit is a secret, she invents a truth serum and forces Russ to spill the beans. She teleports Sacha's invention to the lab so she can sabotage it, not realising she's also teleported Jack. Once alone in the Lab he steals the truth serum, escapes and confronts Elizabeth, using the serum on her.
Toby invents an anti gravity belt that will lift the wearer to any height. But Jack manages to steal the belt and attach it to a small dog, Dudley who belongs to the school's new benefactor, Mrs. Xavier. As Dudley disappears from view amongst the treetops, happily chasing birds, Mr. Woods is left with the problem of how to explain his disappearance to Mrs. Xavier.
When Elizabeth finds that Verity and Garth can't meet her exacting standards as personal assistants, she decides to create a self-learning artificial intelligence program to do the job instead. She calls it Max - and it doesn't take her long to realise that she's created a monster. Max soon decides that he alone knows what is best for Elizabeth and keeps her prisoner in her own lab. He attacks Toby via his computer and spies on Verity and Garth.
Unable to bear the thought of Toby and Nikki getting together, Elizabeth traps Toby in a time loop, forcing him to relive the same day over and over until he accepts the alternate reality she has created for them. In Elizabeth's world, she and Toby have been together for six months, she's given him a new image, he gets 100% in his tests and he no longer has anything to do with his old friends. But Toby wants nothing to do with this new world.
The crimson-ringed octopus has venom so toxic that one drop can immobilise an elephant; or one Mr Woods and one Elizabeth. Mr Woods, hit by a poisoned spitball from Garth, ends up stuffed into a cupboard and Elizabeth, accidentally stung, remains gracefully unconscious on her laboratory floor. Meanwhile, Ms Hammer demands to know Mr Woods whereabouts and Sacha and Verity have to create a diversion plus hide Mr Woods and his mobile phone.
Nadine Sterling, a movie star, has come to Sandy Bay to shoot her new film in the house where the legendary Violet Strickland is believed to have died a horrible death. Meeting Nadine, Russ is immediately in love. The class go on an excursion to the movie set where Nadine, with the help of the film crew, humiliates Elizabeth by scaring her with some hollywood magic. Elizabeth swears revenge and lures Nadine and her new found friends - Russ, Toby and Sacha - back to the house that night.
When Garth's little cousin, Rodney, turns up in Sandy Bay, he immediately causes havoc with his pranks. He starts by spraying Sacha with a water hose and soon goes on to bigger and better things at the school. Sacha gets back at him with itching powder - which he doesn't like. Tinkering with one of Elizabeth's experiments, Rodney is bitten by a spider and emerges from a silvery cocoon as half arachnid, half boy who can spit a high tensile web.
Desperate for information about Elizabeth's genius, Jack offers her a deal. If he can turn his (and Nikki's parents) against Toby causing the couple to split up, will Elizabeth tell him what he wants to know about wicked science? Planning on telling him nothing, Elizabeth agrees and sets out to ensure the lunch with Jack and Nikki's parents is a disaster.
In an attempt to make Toby jealous, Elizabeth partners Jack in an end-of-year science experiment. However, Jack's persistence and undeniable charms are working their magic and when Jack kisses Elizabeth she begins to fall for him.
Jack skilfully convinces Elizabeth to de-genius Toby and she builds a new MFE machine. When Elizabeth leaves to find Toby, Jack powers up the machine and, having already stolen the formula, turns himself into a genius. Toby and Elizabeth return and Jack threatens to de-genius them both.