WARNING: The following contains spoilers for Blade Runner: Black Lotus, Episode 13 "Time to Die," which aired on Adult Swim and is now streaming on Crunchyroll.
Niander Wallace Jr. (Jared Leto) is the primary antagonist of Blade Runner 2049. In the original film, he is depicted as a ruthless CEO and scientist who is obsessed with creating a perfect species of human, having taken over the replicant program from Tyrell Corporation. While Blade Runner: Black Lotus has primarily followed a replicant named Elle aka Black Lotus, the series is really an origin story for Wallace Jr. that specifically focuses on his rise to power -- and how Elle played an important role in facilitating it.
Since Episode 1 of Black Lotus, Wallace Jr. had been working behind the scenes, experimenting with different models of replicants. As recent episodes have revealed, Elle is one of the experiments he created for the sole purpose of murdering his father. Throughout the story, Niander Wallace Sr. had been wanting to shut down the replicant program since he considered it to be a bigger liability to his company than it was worth. He particularly cited the fall of the Tyrell Corporation following the rebellion of a few rogue replicants led by Roy Batty (Rutger Hauer) in 1982's Blade Runner.
With father and son clashing in their goals, Wallace Sr. initiated a Doll Hunt to rid his company of his son's experiments, while Wallace Jr. used it as a trigger for Elle to do his bidding. Elle was completely unaware of Wallace Jr.'s plans as he programmed her to be a high-class fighter who couldn't easily be killed, not even by a deadly blade runner like Marlowe. Throughout Black Lotus, Elle had been murdering everyone who participated in the Doll Hunt, until she finally got to Wallace Sr. and did him in with his own gun. Elle hadn't realized this was all a part of Wallace Jr.'s plan until she learned the truth from Water Lily -- another replicant of a similar model to herself -- and Joseph confirmed this was the case.
With Elle now fully aware of why she exists, she targets Wallace Jr. in the Black Lotus finale, which also compiles the remaining pieces that set up the premise of Blade Runner 2049. It is actually here in Episode 13 that Wallace Jr. starts to display his more identifiable traits as his older self. In the original film, he sells himself as a businessman capable of creating completely flawless replicants who are 100% obedient to their masters and cannot kill their creator.
He demonstrates this to potential clients by ordering replicants to kill themselves, which they do without question. This further establishes Wallace Jr. is not beyond disposing of any replicants he deems useless, and gives limitless capabilities of his replicants for as much as a client is willing to pay.
In Episode 13 of Black Lotus, Wallace Jr. orders Water Lily to fight Elle to determine which is the superior model. Water Lily proves fully obedient and engages Elle in a duel to the death. This obedience to Wallace Jr. proves to be her undoing as she behaves no differently from a robot and ultimately lacks agency. Since Elle has the free will of a real human being, she is able to think for herself and make the kinds of decisions Water Lily can't. This allows her to gain the upper hand on Water Lily and defeat her without killing her.
After witnessing the fight between his two greatest creations, Wallace Jr. determines Elle is the superior model and kills Water Lily himself for her perceived flaws. He then attempts to win Elle over by catering to her past feelings for him and offering to love her for real this time. Having learned more about herself through her friendship with Joseph -- a former blade runner -- than she ever did as Wallace Jr.'s lover, Elle doesn't take the bait.. Since she is physically incapable of killing her creator due to her programming, Elle instead decides to permanently injure him instead. This is when she slices his eyes with her katana, permanently blinding him.
While Elle manages to escape with her life and leave Los Angeles for parts unknown, her actions may have actually motivated Wallace Jr. to become the ruthless CEO he is in Blade Runner 2049. Not only does Black Lotus end with Wallace Jr. saying "I see nothing but limitless possibilities," he may have ultimately decided that Water Lily was the flawless model and made many more replicants to be as completely robotic as her.
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