At the beginning of The Usual Rules, thirteen-year-old New Yorker Wendy is just getting ready for a normal school day. She says bye to her stepfather Josh and her little brother Louie, and misses seeing her mother before she heads off to work. That's for the best anyway, because Wendy and her mother are fighting over the fact that Wendy wants to take some time off of school and go to California to visit her biological dad—who has largely been absent in her life.
When Wendy gets to school, though, the teacher announces that there's been a huge catastrophe: Two planes have flown into the World Trade Center. Wendy is horrified because her mother works in one of the towers. She waits for hours while other students get picked up, and finally Josh and Louie come to get her… but they don't have her mother with them.
Wendy, Josh and Louie walk home and wait by the phone for her mom to call or return. But Janet—Wendy's mom—never comes back, even after weeks. Josh is completely bereft and overwhelmed by the task of taking care of two kids, so when Wendy's father shows up unannounced and says he wants her to come live with him in California, Josh lets her go.
And so Wendy boards a plane and goes to stay with her father, Garrett, in the little town of Davis, where he lives and works as a carpenter. She settles in, but takes on a whole new identity, one in which she's not such an obedient little girl anymore, skipping school and going to the local bookstore or Sacramento instead.
Wendy meets a girl named Violet who isn't much older than her but has just given birth to a baby, a little boy named Walter Charles. Wendy befriends Violet and the bookstore owner, Alan, although she tells them both that her name is Kitty. She spends a lot of time hanging out at the bookstore or at Violet's apartment, and calls her best friend from New York—Amelia—often to get updates on what's going on.
Wendy also gets to know Garrett's girlfriend, a woman named Carolyn who lives on a cactus farm. Garrett takes Wendy to San Francisco one weekend to meet up with her grandmother—his mother—and it's clear that his mother wants them both to be a lot fancier and more refined.
Wendy sneaks out of her hotel room to go wandering in the middle of the night, and ends up befriending a skateboarder named Todd who is a runaway; he's been traveling across the country looking for his older brother, Kevin. She lets him shower in her hotel room, and afterward she gives him her address so he can come visit if he's ever passing through Davis.
Over Christmas, Garrett's mother dies and he has to attend the funeral. Carolyn cooks for Wendy, and some of her friends unexpectedly show up. Alan shows up with his autistic son, Tim; Violet arrives with Walter Charles; and Garrett comes home with a surprise: He picked up a hitchhiker on the way home from the airport, and it turns out to be Todd, who was coming to see Wendy. What a coincidence. So they all spend Christmas together and it's a swell time.
After everyone leaves, Todd stays the night and he and Wendy even spend some time making out. He leaves the next day to go to Colorado, where he has a lead on his brother, Kevin. But he promises to write and call her when he can.
Garrett and Carolyn tell Wendy that they know she's been skipping school this whole time, but they also know she needs to do this in order to cope with her mother's death. In the meantime, Wendy hears from Josh that Louie isn't doing so well. He can't seem to understand that their mother is dead, and he keeps freaking out and throwing tantrums. Wendy also learns that Kate—her mother's best friend—has been seeing Josh. Kate decides to leave New York City for good, though, and move to Hawaii; she comes to apologize to Wendy for what happened with Josh.
Wendy also hears from Todd, who tells her that he finally found his brother and they're living together and working now. He has some semblance of a family at long last. In the meantime, Violet decides that she's too overwhelmed by motherhood and decides to give Walter Charles up for adoption—a decision that upsets both Wendy and Carolyn, who have grown attached to the baby.
For Wendy's birthday, Garrett takes her to San Francisco and to Yosemite and says that he thinks it's best if Wendy finishes out the school year before deciding where to live permanently. This upsets her because she feels like her entire life is out of her control and no one's consulting her. He apologizes and they make up.
Josh sends Wendy a box full of gifts that her mother bought for her before she died, but Wendy is afraid to open it. After going to school in Davis, Wendy decides that she's going to move back to New York City; she tells Garrett she's taking the train home—Louie and Josh need her. Before she goes, Wendy opens the box and sees that her mother bought her a plane ticket to California. Aw, she meant to let Wendy go after all.
Wendy takes the train all the way home without telling Josh and Louie that she's coming. When she gets there, no one is home so she goes straight to Louie's school and picks him up. He's delighted to see her and they walk home together, hand-in-hand.