- Shortly after hatching from her egg, Baton the tadpole is carried by a pelican to the top of a mountain, and she must make her way back home avoiding obstacles and collecting bubbles.
- Baton hatches from her egg at the encouragement of her mother, Melody. After learning to avoid rocks (musical notes) and collect bubbles, she strays too far from home and is captured by a pelican named Coda
While flying near the top of the mountain that makes up Opus Island, Baton whacks the inside of Coda's beak, causing him to drop her into the Trout Tributary. Avoiding fish and bears, Baton finds herself in a rusty pipe with a tortoise named Walt. He mostly ignores her as she collects bubbles, preferring to chomp up the splotches of red food in the pipe. The next area is a strange land called Chiptune Lagoon, where everything appears blocky and the hills in the distance seem to have eyes. As night falls, Baton passes through Midnight Bayou, where another young tadpole named Sonata croons to Baton about how much he loves "baYOUs". They part ways with him wishing her good luck in the path ahead.
After this, Baton is surprised by a small bird that catches her, but is saved by a large bullfrog named Etude who appears to eat the bird in one gulp. Etude tells Baton she can bring him bubbles and "challenge flies" to unlock more features. He also provides light conversation on request. Baton's travels take a dark turn in Barracuda Caverns, where she is relentlessly pursued by a barracuda named Crescendo. She is able to fend him off by jumping out of the water when he snaps, distracting him by whacking light-up mushrooms with her tail, and eventually trapping him in a treasure chest. In Snowfall Lake, Baton has some fun with small banks of snow above the water, but in the middle of the lake, the water becomes very cold. Baton leaves Snowfall Lake in good spirits, though. At Gusty Rapids, Baton is carried downstream by a fast current, and everything seems backwards. Before going over the final part of the waterfall, she passes through a mysterious Badger Temple, complete with rolling rocks, glowing statues, and arrow traps.
In Piranha Jungle, Baton is chased by Staccato and his pack of piranhas who sometimes struggle to get their act together. She is eventually able to distract them by jumping out of the water and whacking low-hanging fruit into the water for them to eat. At the bottom of the waterfall, Baton finds herself in a desert at sunset, in a river known as Thunder Creek, with dinosaur bones everywhere. A stag beetle warns Baton of the harsh waters ahead, suggesting she turn back. Ignoring him, Baton passes some snails, and their leader sings about the dangers of Thunder Creek, giving her some advice, and telling about past water beasts who didn't survive making it through Thunder Creek. Baton avoids the crayfish shooting rocks at her, and makes it to the end of Thunder Creek.
Baton's jubilation at surviving Thunder Creek doesn't last long, though. Thunder Creek feeds right out into Saltwater Cape, which is practically the ocean. She must pass through Saltwater Cape to get back to her home in Tadpole Pond. Choking on the salt water, Baton finds relief by not only collecting food, but also hitting cymbals that launch her above the water, away from the salt. Quite a few times, Coda shows up again, attempting to grab Baton in his beak, but Baton just pounds away from inside every time, making him drop her. She gets to the end of Saltwater Cape and begins the final trek to her home upriver. Baton is happy, as she is almost home free.
But to her shock, she finds her home dark, cloudy, and covered in oil! Nearly everyone is gone. Suddenly, Coda lands in front of her, showing her that the oil has gotten on his wings and is ruining life for everyone. He shows her a crashed airplane, which is the source of all the leaking oil, and explains that only she can fit inside and shut off or destroy the sunken derelict. To get there, she has to hop in his mouth so he can carry her over the oil. Baton ponders this for a moment, and with a new resolve hops in his beak. Coda carries her over and she jumps into the back of the plane, making her way forward through the passenger aisle while strange music touting the benefits of a new autopilot system plays through the plane's speakers. When Baton gets to the front of the plane, she slaps an electrical wire to open the path to the cockpit.
In the plane's cockpit/control room, Baton cuts the wires controlling the fans and avoids the autopilot's buzz-saw attack. When the computer, ELE-94, attempts to kill Baton by lighting the oil bits in the water on fire with a lighter, Baton whacks the lighter back at the autopilot a few times to destroy it. After destroying the autopilot, an explosion sends Baton out of the pooling water and onto the control console.
Without water, Baton flops around on the platform, desperate to breathe. She thinks she is done for when she looks back and notices her hind legs have grown! She jumps out of the plane's cockpit right before one final explosion destroys it, and swims safely for home. Her parents, Melody and Timbre, are waiting for her, happy to see she's returned.
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