Junko was born during a rain storm in the Land of Water.
In the years immediately preceding the founding of the Hidden Villages, Junko's parents lived on a small island in the western Land of Water. Her parents, ninja who had spent time in both the Land of Fire and the Land of Wind, had returned to their homeland in the Land of Water to birth their two children: Junko and her twin brother, Hotaru.
In the early years after the official founding of the Hidden Villages, the Villages were still making efforts, some overt and some quite covert, to recruit unaffiliated ninja. Junko's parents had spent a great deal of time in the Land of Wind where they had learned and mastered the Puppet Technique. Shortly after Junko's third birthday, her parents were approached by ninja from the Land of Wind who wanted to recruit her parents into the nascent Puppeteer Corp. On that day, Junko's parents refused the Sand ninja for the first time. Exactly one year later, the Sand ninja returned for a second time; for a second time, Junko's parents refused. A year later to the day, shortly after Junko's fifth birthday, the Sand ninja returned for the final time. For the final time, Junko's parents refused.
Shortly thereafter, on a day when the morning fog was heavy, Junko's father prepared for a trip down to the closest town to obtain some supplies. The rest of his family stood in front of their home to see Junko's father off. Her father kissed her mother, patted her brother on the head, and bent down to hug Junko before he set off for the town. It was the last day that Junko would see her father alive. The next day, Junko awoke to find her father's body at the doorstep of their small cottage with a note from the Sand ninja: "We will not be denied." Junko's mother did what any ninja in her position would be expected to do: she prepared to avenge her husband.
On the seventh day after the death of her husband, Junko's mother took her children to the nearby town. Leaving them with friendly townsfolk, her mother addressed her children. Her mother told the twins how much she loved them, how proud she was of them, and how she would return after avenging the death of their father as was her duty and honor. She bent to one knee to kiss Junko and her brother, Hotaru, on their foreheads. She hugged Junko tight before she stood and left to find the Sand ninja. Her mother's body would be found three days later.
The townsfolk decided that the two orphaned children should be raised as ninja to honor their parents. The twins, along with their parents' scrolls and puppet equipment, were given into the care of ninja of the Village Hidden in the Mist. Once there, the Village wanted to induct both kids into the Academy. Hotaru was immediately admitted, but Junko's future was less sure. Junko was a frail child, and the death of her parents had left the young girl shaken; her evaluators questioned whether she could ever be a successful ninja.
Since the death of her parents, Junko, along with her brother, have explored the scrolls and puppet tools left behind by their parents. Junko had grasped for herself the rudiments of the Puppet Technique: she was able to form chakra strings to manipulate, in basic ways, the mannequins that stood in the apartment where she lived with her brother. After demonstrating her technique, her evaluators agreed that her sharp intellect and impressive chakra control could provide her a path to becoming a successful ninja in the service of the Mist.
During their years in the Academy, Junko and her brother developed their skills with the Puppet Technique. Though they developed different styles, the two practiced with each other and helped each other to improve their skills in crafting and manipulating puppets. Where Hotaru found kindred spirits in his puppet creations, Junko saw them as tools to practice her craft and to manifest her will. Recently, she has just begun to explore manifesting her chakra through the Water Release, though she is still in the infant stages of that kind of chakra manipulation. Her years in the Academy were filled with her studies during the day and with her endless tinkering during the night. Through it all, her only real connections were to her brother, Hotaru, and to her village, the Mist.
Now, Junko has graduated from the Academy. Recognized as a ninja, her life is focused on learning and improving her skills in the service of the Mist.