During the intro, a news team sets up an interview with a couple of Unikitty's best friends, within Unikingdom, one of 8 major realms in the Lego World (the others of which include Middle Zealand' world, Wild West, Bricksburg, and Cloud Cuckoo Land) which have lived in harmony for years, following the events of both the end of the Kragle Crisis, and Lego Clay War, that both occurred in 2014.
When the reporter asks about Lily Sage, the younger now 10 year old sister of Lawrence Sage, who was also the one who initiated the Lego Clay War, and sent her brother to the Lego World due to the help of magic potion given to her by a Voo Doo Witch Doctor, during the events of LEGO 2 Reunification, who still lives within the real world, and is still constantly always inside Lawrence's bedroom, one of Unikitty's friends cockily describes her as an ugly, simple minded creature who poses no threat to the Lego kingdom anymore, due to her still being grounded after costing her parents 500 dollars in destruction of her 30 pound playdough box that was given to her.
However, Lily is watching the live feed from inside Lawrence's Bedroom and later becomes, enraged by the insults where she, uses a small bucket of homemade clay to pour inside at least five of the major realms, that were placed on Lawrence's play table which in the Lego Universe encases all of its inhabitants including some of the master builders into crystal, and sends out her hordes of Grim Clay soldiers. Despite the apocalyptic downpour of Clay from the giant buckets, Four characters however, Lawrence Sage, Unikitty, Puppycorn, and Emmet, is able to avoid the attack due to them being out of the line of fire, mostly due to Lawrence being on the ground, with Unikitty on top of his back, protecting him, and Emmet who was on the way through the warp gate to Unikingdom at the time.
The four friends then bound together and vows to rescue all the trapped master builders and defeat Lily Sage once and for all. The group visits each of the realms in sequence, freeing trapped Inhabitants and Master Builders, all while collecting special idols that are meant to piece together the old portal to the Reality realm, and also was successful in defeating some of the Grim Clay Higher Ups, within each realms' portal worlds.
They then make their way back to the real world, which they visited 4 years prior in LEGO 2 Reunification, where the final campaign of the Lego Clay War was fought, where the group fights their way through two precursor portals before confronting the giant little girl herself. After they defeated Lily Sage an ending clip shows all three back in Cloud Cuckoo Land this time, discussing their victory with the news reporters.
After the credits, The group of four then appears back in Lawrence's Bedroom again where they free one last dragon who points them to Lily Room that was located across the hall which by now Lawrence, can lead his friends to enter and destroy all traces of clay in order to prevent Lily from conducting anymore assaults on the Lego verse once and for all. Once the Three friends have gathered enough Idols, and power cells to open Lily's door, Puppycorn, decides to stay behind in order to help with the freeing of the rest of the Lego universe's inhabitants, leaving Emmet, Lawrence and Unikitty, now this time accompanied by Good Cop/Bad Cop, in order to be there in Puppy Corn's place in order to venture into Lily Sage's room themselves.
An alternate ending plays where the group of four, start to destroy most of Lily Sage's clay collection in response to most of the damage that she has been doing to Lawrence's Lego set for the past 4 years, and the group are able to return back to Unikingdom.
Upon their return, the group is then interviewed by the news reporters a second time just as another magic spell comes in and clay forms some inhabitants again. Lawrence's last statement is, "Here we go again."