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Warning: spoilers ahead for Episode 17 of Supergirl Season 3, called "Trinity."
A big question on Supergirl ever since the announcement that Lena Luthor was joining the show has been whether or not she would go the way of her brother. Lex is a supervillain on Supergirl, although he's currently serving 37 life sentences in prison and only appeared via flashback. Season 2 revealed that Lena and Lex's mom Lillian went a villainous route as well as leader of Cadmus. While Lena always resisted the pull toward any darker impulses and remained a friend to Supergirl and Co., the events of "Trinity" may point toward Lena finally going full villain a la her brother and mother.
After the events of the previous episode, Lena's secret was out. Kara and the DEO discovered that Lena had been secretly hiding and experimenting on Sam at L-Corp. Understandably, Kara and Co. felt betrayed that Lena didn't share the fact that Sam was Reign, especially given that Reign escaped and joined the other two Worldkillers. The DEO crew demanded to know how Lena kept Reign contained for as long as she did, and she claimed that she used the last remnants of kryptonite from her brother's stash. Kara didn't trust Lena's word that she'd used up all of Lex's kryptonite, so she sent James as Guardian to investigate.
James decided he wanted to trust his lady love Lena and did not check Lena's vault, instead claiming that Lena had indeed used up all her kryptonite. He confessed to Lena what he'd done at the end of the episode, then revealed his secret identity as Guardian. Lena then confessed that she had lied when she claimed the kryptonite she'd used was Lex's leftover stash. No, Lena has discovered how to make kryptonite, and she did it without telling anybody. Uh oh.
Now, on the one hand, it's easy to understand why Lena would want to create kryptonite and not necessarily tell her pal Supergirl about it. Earth-38 has had to deal with rogue and/or temporarily evil Kryptonians in the past when kryptonite would have come in very handy in stopping them. On the other hand, kryptonite can be used against benevolent Kryptonians to take them out, and most of the characters on Supergirl wanted the last of the kryptonite on Earth to be destroyed.
Lena likely wanted kryptonite on hand just in case she needed it, and she did in fact need it to contain Reign. Without Lena's information that she gathered on Reign, the good guys almost certainly wouldn't have been able to take out Pestilence and Purity in "Trinity." Taken on its own, the act of creating kryptonite does not mean Lena is on the verge of becoming a villain.
What may push Lena toward villainy is the fact that Supergirl is not entirely honest with her. Although Supergirl told Lena that she was ready to move past Lena's concealment of Reign, she only did it after she had James break into Lena's vault and James "confirmed" Lena's claim about using Lex's leftover kryptonite. Earlier in the episode, Lena also asked Supergirl her name after Supergirl complained about Lena lying and keeping secrets, which could point toward Lena being sick and tired of not knowing anything about Supergirl.
If Lena discovers that Supergirl is her BFF Kara who didn't have faith in her, it could destroy her willingness to trust others, and that could set her on the path to villainy. We'll have to wait and see. Lena didn't take well to be shunned by Supergirl, and James will have to decide how to handle her bombshell. Could Supergirl be turning Lena into a villain rather than using the Worldkillers as the baddies for the full season?