Two kits, Stream and Earth, have been assigned to try to meditate and communicate with the grass. Their family, a group called the Sisters, believes that while she-cats stay together and sing to the stars, toms are destined to wander the world and be guardians of the earth. While Stream seems to have some success in his meditation, his friend Earth does not, and this makes Earth worried since he knows their wander will begin in two moons. That night, two of the older tom-kits are beginning their own wander, and the Sisters perform a ceremony before they leave.
A storm kicks up, and everyone awakens before dawn as the camp begins to flood. Stream runs off to look for the others and gets lost on a nearby hill; Earth finds him and starts to guide him back down, but on the way, lightning strikes, and Earth realizes that it has struck and killed his best friend.
The following day, the Sisters hold the ceremony to sing the she-kit Haze's spirit to the stars; she had died during the storm as well. Earth is upset that they won't do the same for Stream; his mother Moonlight explains that toms are meant to return to the earth, but it makes Earth wonder if she wouldn't grieve for him if something happened when he was older. During the ceremony, spirits come to visit their friends and family, including both Stream and Haze, but Earth sees nothing. He had once hoped that he and Stream would wander together, or that he would at least be able to speak to his friend's spirit, but he's certain now that when he begins his wander, he'll be entirely alone.
Two moons later, it's just days before the stars will align for Earth's wander to begin. He doesn't feel ready, though: he's having trouble hunting, and when rogues attack him and the cat he's with, he freezes and isn't able to join in the fight. Moonlight tells him of a tom who once stayed with the Sisters for longer than he normally would have, and how the Sisters had bad luck afterward with several of them dying. She insists that he's ready, even if he doesn't think so. The leaving ceremony is performed for Earth, and his wander begins. He decides that he can wander close to the Sisters, and follows them around for a while. He even gets close enough to encounter his sister Ice, but eventually has to admit that he can't stay.
That night, a trio of dogs chases Earth, and he's rescued by a yellow tom named Root. Root instructs him on how to sleep in a tree where he'll be safe, and hunts some prey for him. The following morning they begin to talk about the Sisters, and Root explains that he was mated to one. Earth, seeing how he and Root have the same pelt color and even the same six toes on one paw, realizes that Root is his father, and tells him that Moonlight was his mother. Root agrees to take care of him for a moon or two, and begins by telling Earth that he can be whoever he wants to be - including his name. Deciding to leave the Sisters behind once and for all, Earth looks up at the oak where they'd spent the previous night, and decides that his new name is Tree.
Tree and Root spend two moons together. Although Root had originally said that he was a loner and that this would only be temporary, he suggests they stay together longer, and Tree is happy to be with his father. One day a fox attacks them, though, and Root takes a bad bite that was meant for Tree. He stays with his father until he dies. Tree feels that their love for each other brought this tragic end upon them, and resolves to only rely on himself from now on.
Eight moons later, Tree meets a pregnant she-cat named Pebbleshine. She explains her situation to him, how she got separated from her Clan, and eventually makes the offer to come with her and join SkyClan. Remembering how he was driven from the Sisters and Root's death, he declines. They decide to spend the night together before separating in the morning. Tree is awakened by Root's ghost telling him that they're not safe where they're at: they're attacked by a fox, but manage to drive it off. After they say their goodbyes, Root appears to him again. He tells him he's proud and that the short time together was the happiest time of his life, and tells Tree that friendships you choose can be stronger than kinship. He promises to watch over Tree, and Tree is hopeful that one day he'll find another cat to walk beside him.
Tropes appearing in this novella:
- Almost Dead Guy: Root is fatally wounded by a fox bite, and tells Tree that he wants his son with him when he dies.
- Contrived Coincidence: The protagonist belongs to a group of cats who travel around and don't stay in one place long; they also only allow she-cats to stay with them past the age of six moons, and mates aren't permanent relationships for them. When the main character eventually is forced to leave and begin his own journey alone, he is attacked by dogs, but is rescued by an older cat that happens to be passing through... who, they realize shortly afterward, is his father.
- Dead Guy Junior: This book reveals that Tree's father was named Root, which means that Tree's son Rootpaw is named after his grandfather.
- Dead Person Conversation:
- After singing to the stars for Haze, various spirits come to visit the Sisters, including the recently-lost kits.
- Root appears to Tree to praise him and tell him that he's proud, and to not live his life alone.
- Death of a Child: Two kits die in a storm; one is struck by lightning, while the other drowns.
- A Dog Named "Cat": Some of the Sisters are named after animals: Hawk, Snail, and Spider.
- Don't Look Back: The Sisters make their young males leave at the age of six moons. They hold a ceremony, and after that the young tom is ordered to walk through the night without looking back or stopping. It's part of them leaving their kithood behind and becoming an adult by their standards.
- Epunymous Title: Tree's Roots shows the backstory of the character Tree, including meeting his father Root.
- Extra Digits: Both Tree and his father Root have six toes on one paw.
- Ghost Reunion Ending: Tree's father reappears to him at the end.
- High-Voltage Death: Stream is struck by lightning just feet away from Earth. Earth checks on him afterward and finds his friend's fur standing on end, his body hot and smelling burnt.
- His Story Repeats Itself: Tree's father dies when the two of them fight a fox. Several moons later, a fox attacks him and Pebbleshine, and Tree fears that either he'll die (since the fox would have killed him if his father hadn't taken the hit) or that it'll kill Pebbleshine like the last one killed his father. This time, the two of them are able to fight it off.
- Luke, I Am Your Father: A mutual example, sort of. Root says that he knew the Sisters, and then Earth realizes that the two of them look similar and that they both have six toes on one paw, so Root might be his father. He tells Root that Moonlight was his mother, and then Root realizes their kinship too and tells Earth.
- Never Got to Say Goodbye: When about to leave the Sisters, Earth realizes that he never said goodbye to his sick sister Ice, but with the ceremony starting it was too late. He does later find her again and speak to her.
- Overly Long Scream: Earth's mother Moonlight yowls a terrified "Mrrrrooooooooooow!" during a storm.
- Parental Favoritism: Tree eventually realizes that Moonlight loves his sisters more than him.
- Rescue Introduction: Earth meets his father when Root rescues him from some dogs.
- Series Continuity Error: In this novella, Moonlight says that the Sisters do not sing toms to the afterlife; however, they did so for Flickerkit in Squirrelflight's Hope. However, that novel takes place chronologically after this novella (though was published before), so the Sisters may have made an exception for Flickerkit.
- Strong Family Resemblance: Tree looks just like his father Root, down to their six-toed paw.
- Taking the Bullet: Root jumps in between a fox's jaws and Tree when it tries to bite him.
- Traced Artwork: The image of Tree on the cover is traced from a public domain image
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