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.
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.
After the events of the previous episode, Lena’s secret was out.