CAN LENA BE A LUTHOR WITHOUT BEING EVIL?
Supergirl is concerned with family and legacy more than almost any other theme, and Lena Luthor is the most complicated embodiment of that idea. The adopted sister of Lex Luthor (already defeated by Superman and imprisoned in this timeline), her main ambition is to rebuild the family name by putting L Corp (formerly LexCorp) resources to use for the global good, initially operating under the partial assumption that having been adopted whatever degree her brother and mother's darker tendencies might be inherited traits wouldn't be present in her. Then Lillian showed up with a surprise: Her adoption was actually a cover-story for her actually being Lionel Luthor's lovechild - she's a "real" Luthor after all.
That's made the question of whether or not she can wrench free of her family name both more urgent and complex for two seasons now, and season 3 has leaned heavily on the idea that her best way of helping is less "being good" than putting "bad" instincts (ruthlessness, cunning, deception) to good uses. That more-or-less worked out for her contribution to season 2's big finish (retooling a xenocidal weapon of mass destruction into... well, still that, but turned against "bad" aliens instead of Supergirl), but it's an unresolved issue as to whether or not she can walk that line without tipping over to the dark side - especially if she didn't necessarily see her actions as "dark" in and of themelves.
HOW MUCH DOES LENA KNOW ABOUT SAM/REIGN?
Short version: Lena Luthor's friend and personal assistant Sam is actually Reign, the Krypton-engineered "Worldkiller" currently bedeviling Supergirl - and no one knows this, including Sam herself. She "blacks out" when she becomes Reign, only to "wake up" after with apparently no memory of what she was getting up to during the missing hours. She only just got comfortable/desperate enough to tell her friends about this and get tested for whatever might be causing the problem, but the blackouts are getting worse and now Lena (after intervening when one such "blackout" left Sam's daughter stranded and alone) has caught a glimpse of her other personality during a brief moment of anger. But instead of being confused, Lena was reassuring: Telling Sam "I know what's wrong with you, and I want to make you better."
What does Lena know - or at least think she knows? Has she already worked out that Sam is Reign? Before Sam's eyes went all red, Lena was in the middle of noting that her blackouts have been coinciding with... something, so it's conceivable that she's been ahead of the game for awhile or at least suspected as much. If so, what does "make you better" mean? Supergirl's favorite "Kara versus The Other Good Guys" dynamic is her wanting to save/rehab villains versus someone else wanting to take more extreme action. The decision to make Earth Daxamite-proof (expelling Mon-El) in season 2 was facilitated by her invention making it possible, so does she have another such method for neutralizing the Worldkillers?