After the day of the departed Aria has been spending most of her time finding a way to get the darkness out of Lloyd. She told the ninja she was going on a trip and left.
Meanwhile Acronix, one of the Hands of Time, passes through a time vortex and is challenged to a fight by Master Wu. After the arrival of the Forward Time Blade, Acronix hits Wu with a Time Punch which accelerates his aging one day per hour. Even with the intervention of the Ninja, Acronix escapes and reunites with his brother Krux.
Now the two Hands of Time have a plan that could change history and revert Ninjago back to its old-fashioned roots. They control an army of Serpentine known as Vermillion, from the eggs of the Great Devourer, who can form into Samurai using metal. The Vermillion began capturing Ninjago builsers, including Cyrus Borg, and stealing metal.
All to build the Iron Doom, which can travel time, using the Time Apparatus to utilize all four Time Blades. With Master Wu unable to fight, P.I.X.A.L. offline, three other Time Blades scattered throughout time, and a mysterious new Samurai X to learn the identity of, Lloyd leads the team to stop the Time Twins and save Master Wu. The adventure soon proves personal to Kai and Nya, when it turns out their parents could have ties to the villains.
Lloyd had been struggling with Aria's disappearance, his powers have been acting weird and he's been hearing voices, he really needed her at the time. He's only gotten one letter from her saying that she loves him and that she'll be back soon, she told him to make sure the ninja stay out of trouble and to be safe. In the end the hands of time were defeated with Sensei Wu being lost in time.