The introduction of Lex Luthor to CW's Supergirl has helped to solve many of season 4's apparent plot holes. Superman's arch-nemesis has also restored the momentum of a long-neglected subplot involving a Russian clone of Supergirl, which was meant to kick off an adaptation of the classic Elseworlds tale Superman: Red Son.
The final scene of Supergirl's season 3 finale, "Battles Lost And Won," revealed that Supergirl's battle with the villain Reign resulted in the creation of a clone of Kara Zor-El. This clone was discovered by the military of Kaznia, a fictional nation unique to the DC Universe located in Eastern Europe that shares a border with Russia and used to be part of the Soviet Union. As Supergirl season 4 progressed, infrequent scenes showed the continuing training of the Kara clone and her reaction to global events, such as the anti-alien terrorist group the Children of Liberty seeding Earth's atmosphere with Kryptonite dust.
These scenes raised a number of questions regarding Supergirl season 4's plot holes. It beggared belief, for instance, that the Kaznian military just happened to have built a Kryptonite-proof shelter where the Supergirl clone could wait things out until Lena Luthor fixed the atmosphere. Some eagle-eyed fans also noticed that the Supergirl clone had pierced ears, despite there being no logical reason for the military to pierce her ears, even if they were capable of breaking a Kryptonian's skin to do it in the first place. It was largely assumed that Melissa Benoist didn't remove her earrings before shooting started and nobody noticed the mistake until the episode aired.
"The House of L," episode 16 of Supergirl season 4, explains these and other plot holes, while spinning a flashback story that shows how Lex Luthor has been occupying himself since his imprisonment several years earlier. It is revealed that Lex had a contact in the Kaznian military and that Lex was secretly brought in as a consultant (after making arrangements to hide his escape from prison) to help develop the clone of Supergirl into a weapon they could use to declare war on the United States. Naturally, Lex had his own plans for the clone, which necessitated him creating a distraction in the form of the Children of Liberty, whom Lex indirectly organized through his henchman Otis.
The flashbacks go on to explain just how the Kara clone was saved when the Children of Liberty made the Earth's air poisonous to Kryptonians. With Lex engineering both programs, it was easy enough for him make sure the Kaznians had what they needed to protect their Supergirl while the Children of Liberty enacted their plan. The episode also revealed that Lex had the foresight to pierce the clone's ears while she was weakened, saying that they might need her to impersonate the real Kara Zor-El at some point, so every detail must be perfect. Knowing Lex, that's precisely what he has in mind for his personal Supergirl and the real Kara Zor-El's life is about to become even more complicated.