With the threat of the Hands of Time still looming over the realm of Ninjago. The Time Twins have gathered the four Time Blades and are ready to use them to send the ninja to a place where they can not foil their plans. But something goes wrong and both the Time Twins and the ninja are brought to the world of the warrior clans. the Ninja are separated in the chaos and join the five clans. While the four clans fight Darktail and his kin the search for the fifth clan and Zane is on as the Time Twins continue to plot from the shadows.

After the defeat of the Time Twins and Darktail's kin, the clans must rebuild. The ninja must now settle into their new lives as warriors of their respective clans. But with the returning threat of the Over Lord they must join together once more with another returning ally.