Intro: Leonardo narrates as we open with four figures walking up to a village. As villagers stare, the four figures are revealed to be Leo, Usagi, Gen, and Lord Noriyuki. As they approach a cliff, the view reveals an ancient Japanese fortress with an army encamped around it.
Act 1: Open inside the Turtle Lair. All of the Turtles are busy with their own activities, including Leo who is training with Master Splinter. Suddenly, Ultimate Drako appears with the Time Scepter. As Ultimate Drako raises his scepter, energy encompasses our heroes in a flash of light.
Fade in from the blinding light as we see Leo has been transported to a grassy field on top of a hill. As he explores his surroundings, the ninja discovers that he's been sent to Feudal Japan. Unexpectedly, two riders stumble upon the Turtle and are thrown from their horses. One of the riders, an anthropomorphic swordswoman, attacks Leonardo, mistaking him for a ninja assassin trying to capture her companion. Leo reluctantly defends himself until he is able to gain the upper hand in battle and establishes peace with his assailant. The woman introduces herself as Tomoe Ame, the retainer of Lord Noriyuki (the panda child accompanying her). Just then a group of Mogura Ninja (moles) explode from the ground and attack!
Act 2: As the moles attack, Leo helps Tomoe Ame defend Lord Noriyuki. Tomoe is dragged into the ground by the Mogura Ninjas. With three ninjas left, Leo must defend himself and Noriyuki. Luckily, out of nowhere arrows are launched towards the mole men. Two more riders approach and scare off the remaining Mogura Ninjas. The horsemen turn out to be Usagi Yojimbo and Gen!
Now in safety, Usagi explains to Leo that the evil Lord Hebi has called for the assassination of Lord Noriyuki. Hebi shall favor whichever ninja clan kills the youth. As Leo then explains how he got to Usagi’s world. After a short discussion, Leo decides to help his friend escort Noriyuki to the Shogun, in the capital city of Edo. Afterwards, Usagi will help Leo get to the Battle Nexus so the Ultimate Daimyo can send him home.
Cut to Hebi’s Fortress. As the mole ninjas bring Tomoe Ame to Hebi, they inform the evil overlord of Usagi, Gen, and Leo’s presence. With this, Hebi forms a plan to use Tomoe Ame as bait in order to kill Noriyuki.
Meanwhile, Leo and his companions arrive at a cliff on their way to Edo. Gen explains that it's a shortcut - but the only way to proceed is down the very high and menacing escarpment. Suddenly, a group of cat ninjas attack.
Act 3: Our heroes fend off the cat ninjas, who retreat so a group of their archers can launch a storm of arrows from above. Leo and his friends have no choice but to jump off the cliff into the river below! As they swim to the far shore, the ninjas fire an arrow with a note attached to it. The note informs them that Tomoe Ame is Hebi's prisoner and will be executed. Even though it's obviously a trap, Lord Noriyuki orders his companions to save her or else he'll do it alone.
Later that night, Leonardo and his allies arrive outside of Hebi’s Fortress, which is surrounded by an army of ninjas. Leo and Usagi decide that they'll disguise themselves as Hebi's ninjas and sneak in. Gen will stay hidden with Lord Noriyuki in the nearby forest. Leonardo and Usagi lure some ninjas to the woods, easily defeat them and take their outfits. Usagi is less than happy to be garbed as a ninja, but the two proceed with their infiltration plan.
Usagi and Leo walk into camp and begin climbing up the side of the fortress and easily gain entrance into the castle.
Act 4: Gen and Noriyuki are having supper around a campfire. As they sit, a group of mole ninjas tunnel up and captures both of them.
Usagi enters the prison area of Hebi's fortress and defeats the guards. The samurai finds Tomoe Ame and cuts her free - but as the warriors are escaping, they are met by a large group of guards. Tomoe is taken hostage with a blade held to her throat, which forces Usagi to surrender. The two are taken to Lord Hebi’s throne room, where Lord Noriyuki and Gen are already being held. As Hebi is about to finish off Lord Noriyuki, Leo jumps out from the shadows and attacks. With this surprise, Usagi, Gen and Tomoe Ame free themselves and join the fray. As the groups battle, Leonardo confronts Lord Hebi - noting that it won't be much of a fight since the snake has no arms. In a flash, Hebi encircles the Turtle and then throws him forcefully into a wall (Leonardo notes that arms are overrated). Hebi corners Leo and it looks bad for the ninja until Lord Noriyuki takes up a blade and intervenes. The young Lord tells Hebi to give up as his minions have lost the fight. The reptilian overlord laughs and states that his fortress is surrounded by his forces and there's no way for our heroes to escape.
Just then, the Shogun’s army marches onto the fortress grounds, sounding their horns. Hebi looks out a window, seeing that his troops are being overrun - vowing vengeance, the snake flees. Leonardo moves to follow, but Usagi holds him back, explaining that the evil Lord will not escape the Shogun's soldiers.
Lord Noriyuki bows and thanks Leonardo for his assistance.
The next morning, Usagi draws a pattern on a large standing stone. Once the samurai is finished, he and Leo begin to chant, opening the Battle Nexus portal. With the gateway revealed, Leonardo and Usagi leap through...