Lloyd and the others face off enemies who can control time. In the conflict, Wu is incapacitated, forcing Lloyd to take up a leadership role but he struggles to keep the team in line.
Lloyd and the Ninja are helping Dr. Saunders clean up the museum. Cole finds a painting of the battle with Wu, and Garmadon fighting the Time Twins and tells Lloyd to check out his father. He notes that they are Ninjago's two greatest Elemental Masters, and wonders if he'll ever live up to their legacy. Zane tells them that the painting dates back about 40 years ago, during the Serpentine Wars and Lloyd asks Dr. Saunders what it is. He says that it has no historical significance, and he tells them that "in legend" the Time Twins could manipulate Time.
During Wu's battle with Acronix, a Time Blade falls from the sky causing a temporal anomaly which causes time to skip an entire minute. Lloyd and the others are walking out of the Museum when the Time Blade causes them to be displaced In the Destiny's Bounty 2.0. Zane finds out that there was an energy displacement caused by temporal energy. They also find out that the displacement came from Wu's old monastery and Lloyd suggests that they check it out, and then remembers that Wu went there—so they go there.
When they arrive, they see Acronix alone. Jay goes to fight him, and Zane tells them that it's Acronix from the painting. Lloyd points out that he should be older because the painting took place 40 years ago. The other Ninja go to help Jay and Kai accidentally sets the monastery on fire again. Lloyd orders Jay, Cole, and Kai to help him battle Acronix, and tells Zane and Nya to try and put out the flames.
Lloyd and the Ninja push Acronix back with their powers so that he apparently falls off the edge, but he actually just uses the Time Blade to move forward in time and escape.
Thinking they defeated him, they find Master Wu (who was hanging on a tree branch) and help him back up.
Shortly after their battle against Acronix, the Ninja meet with Wu at the Temple of Airjitzu. Wu says they can ask him anything they need to and they bombard him with questions. He tells them about the Time Twins.
After Wu falls asleep, the Ninja go back to unpacking the temple when they see on the news that a strange samurai warrior is attacking the Borg Store. The Ninja arrive at the store, and roll a digital dice to decide who battles it first. Each time it's there turn, they fail at fighting it so they try doing it all at once. The fight is brought into the store, where another Vermillion appears and starts attacking them as well. However, they are more interested in Borg, and so Zane takes him away once they find their weakness and the Ninja to meet up with Zane, only to find him in the alleyway alone and unconscious.
Back at the Airjitzu Temple, Lloyd and the Ninja are trying to figure out where the Samurai Snakes come from, and they ask Wu, but he only talks in gibberish and sleeps. Lloyd points out that Wu isn't himself and that they need to get Zane back online because he was the only one who saw where Borg went. Lloyd tells the others to reboot Zane and see what they can find out while he stays at the Temple to watch Wu.
After the others leave, Lloyd sits next to Wu while he tries to get better. Wu says that Lloyd seems upset. The former says that as a Master in training, he feels like he should be doing something. Before Wu told him what he was missing, he fell into slumber.
Lloyd continues to watch Wu. He leaves to get something, and Wu tells Misako that he is rapidly aging as a result of the Time Punch. As Lloyd comes back in, Wu tells Misako not to tell anyone of his condition. When Lloyd returns, Wu starts rambling and says that Lloyd should have been there when he fought Acronix. Lloyd agrees that he should have been at his side, and that he failed his Master, and that it can't happen again.
He leaves Wu's side to get the Ninja to make a plan at stopping the Vermillion. He tells the Ninja that Wu is in no condition to lead, and Lloyd steps up as Master before Kai and Jay add "temporary" and "in-training" to his title. The other Ninja want to go and fight, but Lloyd says that they need to develop a plan first, much to the dismay of the others.
Lloyd is going over a very boring plan, and Jay starts messing with him which causes Lloyd to start explaining his plan over again, until Ronin and Dareth come in and say the city is under attack. The other Ninja wanted to go ahead and fight them, but Lloyd says they still need a plan. The Ninja don't want to wait, as Lloyd orders them to stay but they ignore the order and left. Exasperated at their ignoring him, Lloyd goes back to watching Master Wu.
Lloyd starts pacing around the room and his mother asks him if he's worried about Cole, Jay, and Kai. He says he's mad at them for not following his orders, and that he's worried about Wu and how he said he wished Lloyd was with him. Wu wakes up and tells him that he didn't mean he wished Lloyd was there, but the whole team. Lloyd is still upset that the Ninja didn't follow his orders, and asks Wu what he should do next, and Wu falls asleep. Lloyd walks to the window and says that he made a mistake, and that his mistake was being alone. He decides that he should go help the Ninja. When he sees that all the power went out, he realizes that the Ninja should be at the power plant.
He arrives before the others and tells them that he's sorry for not going with them to help stop the Vermillion. The other Ninja apologize too, and Lloyd says that they should go in there and fight the snakes. When they get in, the place looks empty. He asks Zane to detect the snakes, and he finds them disguised as office warriors. They fight the Vermillion while Zane is walking around aimlessly. Lloyd points out that the turbines in the place are just turbo charged electro-magnets, so they can use Zane to use the magnet and take the Vermillion's armor. When they've done it, they fix Zane and fill him in on everything that's happened since he fell unconscious. Then, they see on the news that the snakes are attacking Mega Monster Amusement Park. They get ready to leave, save for Jay, who goes to his parents' junkyard to make sure they are okay.
The Ninja are fighting the Vermillion at the amusement park. They get cornered at the middle of the park when they notice that they're only interested in stealing metal, rather than fighting them.
After Ninjago returns to normal, the Ninja celebrate as Nya and Kai arrive to heal their father.
The Ninja are soon informed of Wu sacrificing himself and being lost in time, as they wonder what to do. Jay takes stance and nominates Lloyd as leader, as he is shocked by this sudden decision as his comrades ask for his decision.
Though initially reluctant, Lloyd then takes up the mantle with his first orders being to bury the reverse Time blade where nobody could find it. He then makes his second order to no matter what, locating Wu.