In the wake of his mother's death in The '40s, thirteen-year-old Jack Baker is sent from his home in Kansas to Morton Hill Academy for Boys in Maine. There he befriends Early Auden, an odd, solitary orphan attending school for free because his father was on the board of trustees. Early helps Jack learn how to row, and the two become friends. Early has memorized hundreds of digits of pi, and sees each digit as having color and texture. To him, the numbers tell a story about Polaris, aka Pi, the first navigator, who leaves his home to prove himself worthy of his name. During a school break, Early persuades Jack to accompany him on a trip up the Kennebec River and along the Appalachian Trail to reenact the story of Pi, which Early believes will lead him to his brother Fisher, a World War II soldier who was presumed dead in France.
Navigating Early contains examples of:
- Bears Are Bad News: A large black bear has been menacing hikers along the Appalachian Trail. It even ripped out one would-be bounty collector's eye. Pi's story features a bear, and Early hopes that following this one will help him find Fisher. When they do find the bear, they watch it maul a man to death.
- Brains and Brawn: Jack and Early take these roles during rowing. Jack does all the physical work, while Early acts as a coxswain. Without Early, Jack finds himself completely unable to row well.
- Cave Behind the Falls: Jack and Early follow a narrow, treacherous path behind a waterfall, where they find a series of small chambers.
- Daddy Didn't Show: Jack's father's shore leave is delayed, meaning he doesn't get to watch Jack's boat race. It may have been for the better, since Jack ends up crashing and sinking the boat.
- Death by Childbirth: Early's mom died after he was born premature, hence his name.
- Desk Sweep of Rage: Early sorts jellybeans to calm himself and help himself think. Once, when he thinks Fisher really is dead, he angrily sweeps all his beans off a table. Jack helps him pick them up.
- Disappeared Dad: Jack's dad has spent the last four years fighting in World War II, which is why he couldn't take care of Jack after his mother's death.
- Doomed Hometown: In Early's story, Pi returns to his hometown, thinking he's finally earned his name, only to find that there's been a raid. Most dwellings are destroyed, and everyone is gone. The only thing left of his family is a shell necklace his mother made. He does eventually find his father.
- Finally Found the Body: Jack and Early find Martin Johanssen's skeleton in the waterfall cave. He was the victim of Accidental Murder by Archibald MacScott, who was angry about losing a marksmanship contest and fired a shot that wasn't supposed to hit him. MacScott couldn't work up the nerve to tell Martin's mother what happened, so he left the body in the cave for over fifty years.
- How Dad Met Mom: Jack's dad was traveling across the country to finish his last two years at the Naval Academy. The train got held up in Kansas, and while he was stretching his legs, he saw his future wife delivering a cake to a neighbor who had just had a baby. He asked, "What's a fella got to do to get a cake like that?" She answered, "I guess you'd have to have a baby." They were married a month later. Jack's father gave up his military career and became a farmer, up until the Japanese bombed Pearl Harbor.
- Lost Pet Grievance: Early's frog Bucky dies a few days into their voyage. Early puts the body on a large, sturdy leaf and sets it adrift in the river. For a funeral song, he sings "Lazy River."
- Scatterbrained Senior: The protagonists stumble upon the home of Eustasia Johannsen, a 100-year-old widow who mistakes Jack for her teenage son Martin, who went hunting fifty years ago and never returned. She tells Jack and Early to start digging her grave, because now that her son is home she can finally stop clinging onto life. Once she realizes her mistake, she sends the boys on their way and goes back to waiting for Martin, who she thinks is still a teenager.
- Suicide by Cop: MacScott, who has lived for over fifty years with the guilt of killing Martin, tries to kill Early and Jack. He chases them into a ravine, where they're cornered by the bear. MacScott fires twice, deliberately missing, provoking the bear to maul him.
- Title Drop: "Navigating Early was as challenging as navigating mysterious and uncharted waters."
- You Can't Go Home Again: Traumatized and wracked with guilt over the deaths of his fellow soldiers, Fisher let everyone think he was dead. He secretly travelled back to America and became a lumberjack, working alone in the woods. Early only knew he was alive because he happened to be in the background of a picture that ended up in the newspaper Early reads.