The episode starts with the Ninja trying to find Evil Julian, Randy then gets a phone call from Howard Wienerman and was tricked into coming to his house. Meanwhile, McFist was searching for the Ninja by looking through the window in his office until Viceroy informs McFist about a monster alarm being put in Norrisville High. Once Randy Cunningham reaches his house, Howard informs him about Randy's family moving out the day later. Randy Cunningham, out of surprise and confusion, faints.
When Randy wakes up, he realizes that he only has that day to rescue Norrisville High from Evil Julian, he sneaks out of the window and discovers that Evil Julian was amassing his power in Mount Chuck. Once the Ninja reaches Mount Chuck, he digs a small hole from above, which allows him to see through. The Ninja then sees Evil Julian absorbing power from the Land of Shadows, he then consults the NinjaNomicon to help him on this problem. The NinjaNomicon then shows a few moments that led up to this situation and then teaches him the lesson: 'When facing an unbeatable enemy seek an unlikely ally.'
Randy gets shloomped out of the NinjaNomicon, by falling into a hole, and then receives a phone call from Howard. Randy then thinks that the NinjaNomicon meant Howard as the 'unlikely ally', so Randy tells Howard to come to Mount Chuck. When the call ended, Evil Julian was standing behind the Ninja, ready to attack him, the Ninja and Evil Julian then falls into the inside of Mount Chuck. Meanwhile, Howard was waiting for the bus to Mount Chuck. Evil Julian, then, summons a giant monster from the Land of Shadows to attack the Ninja.
After that, Howard arrives at Mount Chuck and the Ninja tells Howard to help defeat the monster. During the fight, the Ninja realizes that Howard might not be the 'unlikely ally' the NinjaNomicon was talking about. Then, after the duo run around trying to escape the flames from the fire-breathing monster, Howard decides to retreat to the Land of Shadows with the Ninja.
After that, both Howard and the Ninja appears in the Land of Shadows, they then meet Julian and asks him if he knows a way out of the Land of Shadows. Meanwhile, Evil Julian starts attacking the students of Norrisville High and absorbs all of the Sorcerer's power using his own power ball. The Ninja then asks Julian if he knows about a portal back to Norrisville, but in reply, Julian says he doesn't know, but Tyler, a gargoyle's skull and Julian's 'friend', does. The trip from Julian's rock island to the cave of where the portal lies was a pretty hard journey for the three boys, especially for the Ninja.
They eventually find out that the portal back to Norrisville is inside the mouth of a horned beast, the Ninja then gets back to Norrisville while Julian and Howard decides to stay, the Ninja then discovers that Evil Julian uses the Sorcerer's power balls to take over the world. The Ninja then realizes that the NinjaNomicon wanted the Ninja to ask for help from the Sorcerer, the Ninja then frees the Sorcerer and asks for his assistance, the Sorcerer agrees and helps the Ninja defeat Evil Julian.
When Evil Julian was defeated and the Sorcerer in full power, the Sorcerer decides to destroy the Ninja. Before the Sorcerer was able to land one last blow onto the Ninja, Howard Wienerman and Julian gets out of the Land of Shadows and into Norrisville. Thus, giving the Ninja a chance to recover and form a plan. The Ninja finds out what he needs to do and locks the Sorcerer's power balls back in the hole where the Sorcerer was kept a prisoner, then locks the prison again. Everything was back to normal and the Sorcerer meets up with his former self and gets turned into ashes as he ascends to the afterlife.
The next day, Randy and Howard were seen to be saying their final goodbyes. Twenty minutes later, Howard discovers that Randy's parents bought the house next door and invites him over. We then, for the first time, hear the Creep speaking, and he said "You enjoy those snacks, Ninja. Your greatest battle is just around the bend." and then the episode ends.
- Running Gag: Randy been splashing with water two times.
- The title is an allusion to the phrase, "All's well that ends well."
- This episode was not promoted as the Series Finale.
- The Creep speaks for the first time, saying that Randy's battle as the Ninja is not over yet. But it is unknown whether the show is renewed for a third season or whether Randy has to battle another new antagonist.
- This is the first episode where someone non-robot actually dies. The Sorcerer reunites with his good human part and turns into ashes, and Randy incinerates the monster that Evil Julian summoned.
- The final battle against the Sorcerer that the Nomicon told Randy about comes true in this episode.
- This is Randy and Howard's first time going to the Land of Shadows.
- The monsters and statues from the Land of Shadows have an Aztec/Mayan style.
- The Nomicon shows scenes from previous episodes, including "Randy Cunningham: 13th Century Ninja".
- This is the second time that Randy breaks his sword. The first was Sword Quest.
- In a cameo, S. Ward Smith, from inside a cage, insults him for it, as he did every time Randy destroyed a sword-substitute in "Sword Quest."
- This episode is when Randy moves beside Howard's house.
- When Howard talking to the bus driver it was similar to the unseen adult voice in Peanuts.
- The scene in which Viceroy is bouncing a wall off the side of his cage is a reference to the 1963 movie, The Great Escape, in which Steve McQueen's character, Hilts the "Cooler King," similarly bounces a baseball while in solitary confinement.
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