Sonny is severely injured after a fall, forcing a move to a desk job. Jerry and Lou have to leave Skippy behind. Dave and Kate try to make the 'Roo happy but Skippy runs away. The Hammonds must find a way to return to the reserve.
Sonny and ranger Dave notice something amiss about the birds at the reserve. Skippy tries to help but Frank and Jeff, who are removing exotic species to sell, avoid detection. But the criminals are tripped up by their own ineptness.
Lou, as a science project, develops a transmitter and pretends to make Skippy talk. Two blokes, Alec and Bill, fall for it then kidnap the kangaroo thinking it will make them rich. Tike, a lost dog Jerry found, helps to locate Skippy.
Jerry and Lou are captivated by their new friend Chris and his cool dirt bike a gift from his wealthy father. They learn that Chris has no regard for rules, persisting in tearing up the forest. The siblings decide to teach him a lesson with Skippy's help.
A dog is going after the chickens with Jerry and Lou concerned it might be their friend Elyse's dog Buster. But things take a sad turn for Elyse who wanted to be a vet but Kate explains how life works concerning animals.
The Hammonds meet up a family who travel by caravan and put on shows featuring snakes. Daughter Emma becomes friends with Lou and confesses she's tired of moving around. She runs away and Skippy's help is needed to find her.
Sonny takes Jerry fishing leaving Lou behind which she resents. While in the reserve with Skippy she meets runaway Jim who's setting snares to catch food. He think his family thinks he's dumb so he and Lou bond over feeling left out.
Jerry and Lou go along with Kate after her grandad chained himself to a fence to protest river pollution. The rangers are collecting evidence that a mill is killing the wildlife and the kids must keep Skippy safe from contaminated water.
Jerry is teased by his mates for hanging out with Lou so takes a dare concerning recluse Kevin. Kevin is annoyed by the boy but is more concerned about his koalas and their care. Brendan's habit of playing with matches lead to disaster.
Skippy hides when the Hammond family take a boating trip but then gets left behind. Skippy is found by Miranda, a young wealthy girl, who refuses return the kangaroo. Jerry and Lou concoct a scheme to get their pet back.
Jerry has taken up running and is good which threatens Brendan Clarke who is used to winning. Pushed by his father to achieve Brendan resorts to cheating for his victories. Jerry, Lou, and Skippy work to expose the truth.
Kate's brother Sean is visiting but doesn't get along with his critical Grandad. Sean takes Skippy with him and they discover the neighboring children are stealing food because their mother is gone. Grandad may have a solution.
Lou thinks she sees a rare wallaby when they also meet a deaf girl Andrea, who is there with her zoologist mother Bridget. The sign language they learn comes in handy when Lou gets lost looking for the scarce animal.
Lou learns about places that don't have fresh water so she and the other students have a fundraiser. They will jump rope to raise money but the two teams have a competition that turns harmful until Skippy helps.
Eleanor, Jerry and Lou's grandmother, is visiting bringing with her a love of orchids. Her precise ways worry Sonny and land her grandson in hot water. Jerry with Skippy's help finds a rare flower but his effort to please his grandmother go awry.
Jerry and his pal Tim find lost golf balls where they meet young golfer Brad. He gives them lessons and Tim has talent so when he learns Brad quit school early he was ready to do the same. An accident to Brad changes everything.
Cockatoo Squawker, star habitat attraction has drawn a flock of noisy birds annoying the neighbors the Samsons. Jerry and Lou befriend Janine, confined to a wheelchair. A picnic at the swimming hole helps everyone learn something.
Famous wildlife presenter Greg, an old friend of Kate's, arrives at the station to film some rare birds. Sonny and the kids worry about a possible romance. An injury to Lou leads Skippy to ruin the photo shoot but help rescue Lou.