- BIONICLE's Big Bad, Makuta Teridax, ended up becoming the universe itself and enslaving everyone in it at the end of the "Mask of Life" saga, which also marked the end of the original major Myth Arc. So yes, while the Toa managed to fulfill their mission set up eight real-world years before, namely to awaken the Great Spirit Mata Nui and thus save the universe, Makuta possessed Mata Nui's body in the nick of time. Also counts as a Sudden Downer Ending, because this was all revealed in the final chapter of a novel and on the last pages of a comic, while everyone was celebrating.
- To a lesser extent, the Barraki. Their main goal during the 2007 storyline was to get the Mask of Life so they could reverse their mutations, escape the Pit, and return to land to start reconquering their territories. While the mask eluded them and they were re-imprisoned, they were all later paroled by the Order of Mata Nui for more manpower to fight the Brotherhood. While Caparar died, the others survived both the war and Teridax's reign over the Matoran Universe, escaping to Spherus Magna and, thanks to Mata Nui using the Ignika's energy to restore the planet, also had their mutations cured as a side-effect with the perk of becoming amphibious on the side. Before the storyline ended, they were looking to set up shop on Spherus Magna with their new armies and carve out some territories for themselves, and looked to be ready to become part of a new Big-Bad Ensemble. Unlike nearly every other villain, they actually ended the story much better off than when they started.
- The Big Bad of the Sons of Garmadon arc in Ninjago successfully revives Garmadon as an Evil Overlord and conquers Ninjago by his side.
The Bad Guy Wins / Toys