Winds of Zion is the third story included in Weed Gaiden, involving the story of Kenta's family and the puppy Zion. It shares many similarities to the first part of Shiroi Senshi Yamato such as both the protagonists being white Akita Inu puppies, both meeting young boys and becoming friends with them, and both helping the boy defeat his bullies by defeating the bully's dog and giving the boy courage.
A father and his two sons are on their way home from the amusement park when their car almost runs over a stray puppy carrying a slice of bread. The puppy shows strong will, not even releasing the bread as he jumps to his feet and hurries to where his mother is waiting up the steps toward the Touunji Temple's grove.
The younger son, Kenta, is a crybaby who constantly gets picked on by two larger kids at his school. The pup's bravery and devotion to his mother endears him to them, and he starts to feed them every day after classes. He names the puppy Zion, and the mother Shiro. Through their daily meetings, Zion quickly befriends and grows attached to Kenta, always answering him when he whistles for them.
One day after school, the bullies tail Kenta and find out about the strays. When Shiro and Zion run off before they can catch them, they turn on Kenta instead. Zion and Shiro suddenly return and defend Kenta, and the bullies make a run for it, comically tripping down the stairs.
The story reveals Shiro and Zion's past: Shiro was originally an abandoned pet by the name of Kinumaru, and while living on the streets met a stray Siberian Husky called Billy. The two had a litter of nine puppies together, and relocated to the grove ground of Touunji Temple in order to raise them. One day, Billy left and never returned. The pups died one by one, until only Zion was left.
Meanwhile, the father realizes what Kenta is doing, but allows him to continue feeding Shiro and Zion. No sooner has he left when the older brother, Yousuke, overhears the news that his mother has cancer and will not live for more than another month. For the moment, neither he nor his father tell Kenta the truth.
As time passes, Zion starts taking the pot Kenta uses to feed them, carrying it and the food it contains into the grove. Realizing that something may be wrong with Shiro, Yousuke and Kenta hurry to investigate. They arrive to find that Shiro has died, the emptied pots lying around her head. Yousuke and Kenta bury Shiro in the grove grounds, to prevent the crows from eating her corpse.
Yousuke and Kenta visit their mother, and take her outside to see the sakura flowers. After asking Kenta to take care of Zion, she passes away in her sons' arms. After the funeral, the bullying seems to get worse. When Kenta comes home with gum in his hair, Yousuke and their father worry about his safety and follow him to the temple's grove.
At the grove, the bullies return, bringing a large dog called Lad to attack Zion. Determined to save Kenta from the bullies, Zion fights against Lad relentlessly until he finally drives the dog away. Impressed by Zion's courage despite being so much smaller than his opponent, Kenta works up his own courage to stand up to the bullies and stop them from abusing Zion any further. The bullies are driven off, but Zion disappears.
Soon, the family has to move away. In the time between, Kenta has befriended the bullies, and enlisted their help in finding Zion. Unable to find the puppy, they leave without him. Zion is discovered to be alive and well, back to scrounging the streets for food.