Usagi, several years prior to the series, was invited to compete in the Battle Nexus Tournament. While carrying water one night, he witnessed the current Battle Nexus Champion, Splinter, coming under attack by Drako (whom Splinter had beaten earlier) and a gang of shadowy assassins. Usagi quickly jumped to his aid until the Daimyo intervened and banished Drako for his treacherous attack.
An unspecified number of years later, Usagi and his friend Gennosuke returned to compete in the Tournament. In the Hall of Champions, Usagi witnessed Leonardo, who was attending the Tournament along with his brothers for the first time, come under attack by the same assassins he had encountered years ago and came to his aid. During this fight, Usagi and Leo formed a friendship which would endure even when they were pitted against each other in the arena. Right in the middle of their match, however, the Ultimate Ninja decided to set his plans to claim the Battle Nexus for his own and take revenge on Leonardo in motion and poisoned Leo with a blowgun dart.
Even though initially distrusted by Leo's brother Donatello, Usagi maintained his calm and eventually ended up fighting side by side with Donnie against the shadow assassins, who were trying to kill both the weakened Leonardo and the Daimyo. This event gained the brainy turtle's acceptance. He subsequently joined the Turtles, Splinter and Traximus in their attempt to stop the Ultimate Ninja and Drako from getting hold of the Daimyo's War Staff, and after the crisis was resolved, he and the Turtles, especially Leonardo, parted as friends.
Usagi and Leonardo would later cross paths when the latter was transported to Usagi's world by Ultimate Drako and inadvertently got caught up in Lord Hebi's attacks against Lord Noriyuki. Usagi and Gennosuke came to Leo and Noriyuki after the Mogura ninja captured the latter's bodyguard, Tomoe Ame. After sending their attackers in retreat, Leo explained his predicament before realizing he could go to the Battle Nexus to ask the Daimyo for aid in finding his family. Usagi agreed to help him open a portal to the Battle Nexus in exchange for safely escorting Noriyuki to the capital of Edo, where Hebi would dare not strike. Unfortunately, Neko ninja pass along a message, revealing that Tomoe Ame was due to be executed by Hebi. Despite Leo warning that it was obviously a trap, Noriyuki made it his intention to rescue Tomoe Ame. Leo and Usagi then infiltrate Hebi's castle disguised as his own ninjas, to the latter's discomfort. Unfortunately, Usagi, along with Gennosuke and Noriyuki, were captured, but Leo's intervention, as well as the time arrival of the Shogun's army forced Hebi to retreat.
Afterwards, Usagi was thanked by Leo and decided to accompany him on his journey to the Battle Nexus, since they were friends. The pair ended up falling into a trap set by Ultimate Drako, who imprison the pair in an arena to fight an army of zombie warriors. Thankfully, Splinter is able to use the War Staff to summon Leo's brothers, who wrest the Time Scepter away from Ultimate Drako. The two staves then react and restore everything to normal. Usagi is then returned to his proper dimension by Lord Simultaneous.
Later, he visited the Turtles in New York at Splinter's behest, hoping that, as one of Leonardo's most trusted friends, Usagi could talk sense into him, since the thought and subsequent trauma of having failed his family during the last battle against the Shredder was leading him into a self-destructive path. Unfortunately, their visit turned chaotic as Gennosuke went out into the city in broad daylight, causing panic, as well as a bounty hunter sent by Hebi was seeking Leo and Usagi.