The Ninja helped clean the museum, and after finding a picture of Garmadon and Wu forty years ago, they decided to ask Dr. Saunders about it.
When they're off, an energy displacement caused them to be relocated on the Bounty. P.I.X.A.L. told them the source is at the monastery, where Wu was, and the Ninja took off.
They eventually encountered Acronix and fought him. Afterwards, they saved Wu before he could fall off the mountain.
The Ninja asked Wu about their fight with Acronix. Afterwards, they left him so he could rest. They discussed the painting they saw on the museum and how it relates to Wu's flashback.
After a while, the Ninja watched a news channel reporting a Vermillion Warrior wreaking havoc at the BorgStore. They decided to attack it one-on-one, but failed, noticing the Warrior could regenerate. Coming to the conclusion that the Vermillion might try to kidnap Cyrus, the Ninja tried to help him. However, they found Zane unconscious and Cyrus Borg missing.
After failing to figure out what the Vermillion helmet does, they went to see Wu for answers. He was unable to answer, however, so Cole, Jay, and Nya went to reboot Zane in the Samurai X Cave while Lloyd stays with Wu and Kai goes to the museum.
They discovered a video feed and slowed it down to reveal Zane being hit by something. After slowing down the video more, they discovered Acronix and Dr. Saunders working together. They rushed to the museum to stop Kai, but Jay and Cole stayed behind to battle with the Vermillion Warriors. When he failed to control his Earth Punch, the Vermillion Army left, leaving them confused.
They went back to the Cave, and found Zane rebooting.
As Cole trained with Jay, he got angry and said he wanted to fight. After he told Kai this, Lloyd came out to tell them he will be their new Master until Wu feels better. However, when Lloyd suggests they make a plan, they reluctantly agreed.
When Ronin and Dareth came to tell them the Vermillion are stealing metal, the Ninja left.
After a brief fight, the power went out and the Ninja met Lloyd at the power source. They created a magnet to attract the snakes' armor, rendering them vulnerable. The power went back on, and they heard the Vermillion are attacking Mega Monster Amusement Park. They left for the park.
At Lloyd's command, Cole and Zane went to help the people on the roller coaster. When he grouped up with the others, they realize they haven't seen Jay since they left for the amusement park.
When time slowed down, the Vermillion Warriors left the park. They figured another Time Blade has arrived, and Zae gave out its location. They left and try to get there before the Vermillion do.
Nearing the Time Blade, Raggmunk threw snakes at them to make them crash. When they tried to get it, Blunck shot them with the Time Blade, slowing them down. However, they are freed right before the Vermillion could attack them.
The Army and Ninja were slowed down right when Jay came to save them. He managed to free everyone from the time bubble. They fought for the Blade and managed to escape with it.
After messing around with the Slow-Mo Time Blade, Jay, Cole, and Zane notes how Kai and Nya are acting strangely. He then agrees with Jay to run toward each other and use the Blade to slow them down before they collide.
Lloyd told them they were supposed to hide the Blade, but they disrespected him. Wu told them the same thing Lloyd did, but they obeyed him instead.
A moment later, they were attacked by Vermillion. They were easily defeated, but it regenerated into Buffmillion, which Nya and Kai were able to defeat.
When Lloyd went down with his Dragon and was unable to summon it again, the Ninja watched as Samurai X saved him. They tried to find out who the Samurai was, but to no avail.
When the twins attacked them, Zane, Cole, and Nya had to fend off the snakes. They eventually got both the Blades, but it was stolen by Machia when they least expected.
They mourned over their defeat and blamed their overconfidence.
Lloyd tells the team that if they can find the location of the Time Blade, they would be able to know the headquarters of the Vermillion Army. Misako then explains Wu was hit with the Time Punch. They left to go to the museum.
Once there, Cole accidentally made a hole in the wall with his Earth punch, revealing a secret room. He found a door, which lead to a sewer system.
After riding on the Destiny's Shadow, Jay and Cole attacked Skales and Skales Jr. but was stopped by Lloyd. They told them that the Vermillion are strong in numbers, and they are located in a swamp. Skales gave them a map and they drove off.
Once they reached the swamp, they noted how many armor and eggs there are.
Lloyd explained that Cole and Jay will rescue the workers. They used a grappling hook and found the workers, along with the Royal Blacksmiths and Karlof. They decided to rescue them by Airjitzuing their way up to the skylights.
Since Karlof is too heavy to hold, Cole suggested they make a ladder instead. He then asks his father where the armor design came from. Lou answered it came from a blacksmith.
When Jay caused the ladder to collapse, the sound alerted the Vermillion. They were eventually outnumbered, but Zane and Lloyd tried to help them.
When the Ninja are being pursued by the Vermillion, they took cover in an Ice dome made by Zane. When Zane decided to save Borg, Cole and the others went with him. After hiding from the Army, they tried on disguises to sneak into the Dome.
Once they met Cyrus Borg, he explains he was forced to build the apparatus for the Iron Doom, allowing the Time Twins to travel through time. They were told he added a code for self-destruct, but had forgotten it. Cyrus told them if he saw the panel, it would probably jog his memory back. They were about to take him, but the Vermillion stopped them. Cyrus was able to convince the Vermillion he just wanted to see if the apparatus is properly installed, but Jay blew their cover. Samurai X came and ran over several Vermillion with the Samurai VXL. Cole helped fight back the snakes as Samurai X brings Cyrus to the panel.
As they fought, Zane figured out the password and Machia's ship arrives. Cole tries to fight back the Vermilion, but Acronix froze Zane, Samurai X, and Cyrus. When they were kicked off the platform, the Ninja caught them.
As the Iron Doom traveled to the future, Cole and the others stayed behind and noticed that Ninja was changing forms before noticing Zane was shut down for some reason. They then noticed Ray was rapidly aging and began worrying for their friends.
Cole soon noticed that everything was changing back to normal as well a Temporal Vortex that Kai and Nya fell out. Cole watched them cure their father of the time punch and wondered where Wu was before realized he stayed behind to settle things with Time Twins.
Though happy at their victory, Cole couldn't help but be worried when his master was feared to be lost in time with their enemies. He and the Ninja elect Lloyd as their master and he makes his first order to bury the Reversal Time Blade and to discover what happened to Wu.