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Following his failed infiltration of the Sons of Garmadon, Zane has learned that Mr. E is also a Nindroid, and the pair face off in a brutal battle that leaves Zane badly damaged. The other Ninja eventually arrive and recover him, and place him in the ship's medical bay in hopes that he and P.I.X.A.L. can work together to restore him. In order to hide from the Sons of Garmadon, they sail the Destiny's Bounty 3.0 into the Dead Man's Squall, a massive storm system. Along the way they struggle with the latest addition to their crew, the babyCole rescue from the Sons of Garmadon who is supposedly the key to finding the final Oni Mask.
Cole eventually discovers that the baby is wrapped in a map indicating the mask's location, which the active Ninja and Harumi study over dinner. Unbeknownst to them, a spider-like creature or robot has been implanted in Zane by Mr. E, and it escapes and begins wreaking havoc with the Bounty. It also manages to infect P.I.X.A.L.'s systems, and she reports that Samurai X is approaching in a large mech. When the Ninja question how this could be a problem, P.I.X.A.L. confesses that she is Samurai X, and that the corruption to her system means that the mech is not on their side.
While Nya searches for the intruder and Jay holds off the lightning from the storm, Lloyd leads the rest of the Ninja in attempting to fight off Samurai X after it takes out one of the engines. The mech eventually takes off with Harumi in it's grip, and Lloyd hops aboard in an effort to rescue her. Samurai X's body then returns to the Bounty to continue the attack, and succeeds in destroying the last engine just before P.I.X.A.L. is able to reassert control. Zane recovers in time to take out the intruder, and Nya is able to use her mastery of water to slow the Bounty's descent to a survivable rate.
Lloyd, meanwhile, is able to place Harumi inside the Samurai X Mech to protect her from the impact of crashing to the ground, and slows his own fall using the map that Harumi had picked up from the dinner table. The two then find themselves in a vast jungle, quite some distance from the fallen Bounty.
Samurai X's line "There is no P.I.X.A.L., there is only the Quiet One!" is similar to lines spoken by other possessed characters in various media, notably including the first Ghostbusters film's "There is no Dana, there is only Zuul."