The Council of the Crystal King is a council brought together by Harumi to serve the Overlord, who is now known as the Crystal King. The producers wanted to include modern concepts within the show, so they were looking for a catchy pop song. Nya (voiced by Kelly Metzger) is the grey/blue ninja, Elemental Master of Water and the original Samurai X.

Tommy Andreasen explained that the character of Nya was employed as an emotional reason for Kai to get involved because, "he didn't want to be a ninja, but his sister was kidnapped by this evil Lord from the underworld". He appears in Ninjago: Day of the Departed, and finally in Crystalized, he is recruited by Harumi to join the Council of the Crystal King only to be shocked unconscious by Jay after the latter reclaims his weapons. It focuses on Jay as he and the ninja enter the video game Prime Empire to face the misunderstood Unagami. Administration Agents are amnesiac agents who hail from the Administration, a parallel realm of the Realm of Madness. In 2017, Lego design manager, Michael Svane Knap commented, "It’s always important to develop good characters that engage with the kids and encourage them to watch.Season 3 focuses on Zane as he and the other Ninja fight to defeat an ancient evil reborn as a new, technological threat.

The show is largely set in the fictional realm of Ninjago, a place loosely inspired by East Asian myths and culture. Lloyd makes his debut in the first season following the pilot episodes as a mischievous child wanting to be an evil warlord like his father, which results in childish schemes that are foiled by the original four ninja.Like the other two commanders, Machia is able to control the Vermillion by communicating with their hive mind. They capture Wu and the ninja in Season 9, but eventually turn against Iron Baron and befriend the ninja. Both the Lego theme and the series had an intended shelf life of three years with the second season planned as the original ending. Other initial concepts for the enemies, such as snakes and robots were rejected, but then used later in subsequent seasons of the series.

In 2009, The Lego Group proposed to make an original intellectual property about ninja, which focused on four ninja with elemental powers. Fugi-Dove (voiced by Adrian Petriw) is a Kryptarium Prison inmate who claims he is the ninja's "frequent and well-known archenemy. Plundar (voiced by Adam Trask) is a member of the Upply and an expert thief who determines all of his decisions through a set of dice.The series concluded on October 1, 2022, with the second part of the fifteenth season being released on Netflix in Australia and New Zealand. The skeletons were considered to be the perfect adversaries for the ninjas because they looked inherently evil and fantastical. Nadakhan (voiced by Scott McNeil) is the main antagonist of Season 6, the Djinn leader of the Sky Pirates and captain of Misfortune's Keep. Misako (voiced by Kathleen Barr) is Garmadon's wife and Lloyd's mother who works as an archaeologist. Unagami is aided by the Mechanic in the real world of Ninjago City to open a portal between Prime Empire and the real world.