Many years ago in the Hidden Kingdom, animals and humans lived in perfect harmony until an evil trickster named HighRoller arrived and fooled the animals into thinking humans were their enemies. Chaos reigned in the Hidden Kingdom until Commander ApeTrully formed a task force called Big Green to reunite the animals and humans while fighting the forces of High Roller and the Zebra Brothers.

The storyline in a typical episode follows a formula, although the formula varies and several episodes depart from it: Commander ApeTrully goes on a mission to the castle of an animal kingdom to make peace and ask its inhabitants to join Big Green, bringing a gift of gold as a token of goodwill. The animals generally dismiss the gift, and usually capture ApeTrully who calls for help from First Squad. Members of First Squad (usually everyone except Mr. No Hands, who does come along on occasion) deploy by descending through a maze of tubes and landing on turtles fitted with tank treads, and then are launched through a tunnel and out over the water. When they arrive where ApeTrully is being held, a battle or contest ensues, during which special talents or abilities of the animals are revealed, often something based on their nature. After the battle or contest, the animals usually concede to First Squad's skills saying through translation by ApeTruly (unless the animal rulers can talk) that they would be honored to join Big Green. After joining, the animals often are assigned a particular duty at Big Green based on their demonstrated skills, which may help solve a problem introduced in a subplot.

The show is very loosely based on ancient Chinese novel the Water Margin focusing on the exploits of First Squad and Second Squad.