Spaulding replaced Oliva as director for the sequel Justice League: Throne of Atlantis, based on the Justice League/ Aquaman storyline of the same name also by Geoff Johns. Oliva then directed the film Batman vs. Robin, released in 2016, before joining Zack Snyder in storyboarding his live-action film Batman v Superman: Dawn of Justice, set in the DC Extended Universe. Oliva returned to directing for Warner Bros. Animation with Batman: Bad Blood.
In 2016, Oliva directed Justice League Dark, the first animated DC movie with an R rating and would be released digitally on January 24, 2017.
Throughout 2016, Oliva was splitting his time directing for WB/DC animated films and storyboarding live-action films and commercials. However, by August 29, 2017, Oliva clarified he is no longer working for Warner Bros., thus making Justice League Dark his final work with them and DC.