Meet Bluey and Sheila, one of the 13,000 little penguin couples who live on Phillip Island, off the coast of Australia. As the devoted penguin couple returns to their cliff-top home to begin the annual breeding cycle, Penguin Island introduces the dedicated team of rangers and scientists who will monitor and protect them through the hottest summer on record.

Long-time penguin couple Bluey and Sheila are struggling to feed their hungry chicks, Sammy and Tom, and protect them from predatory gulls, domestic pets and a feral fox, which is stalking the colony.

Time is running out for hungry penguin chicks Sammy and Tom, whose parents Bluey and Sheila must swim further and further out to sea in a desperate attempt to find fish.

A punishing heatwave hits the island. As bushfires are raging around the state, penguins are collapsing from heat, hunger and exhaustion. The penguin study group finds many heat-stressed penguins and, as the animal hospital fills with overheated wildlife, rangers work to rehydrate and cool the little penguins in a battle to save their lives.

Unlucky-in-love Rocky finally finds a mate in Jess, whose previous clutch of chicks has died. However, it is very late in the season to be raising chicks before the little penguins' annual moult prevents them going to sea. In the burrow next door, Spike and Tash's chicks already are preparing to head off on their own.

Rocky and Jess's lone surviving chick Tilda is not yet big enough to feed herself and is anxiously awaiting the return of her parents. But time is running out as penguins around the island begin to moult and unfortunately Tilda is abandoned by her mother, leaving only her father to feed her.