Lena Luthor....

thats kind of... the point

While there are certainly all sorts of villains they can use and ways to tie her to whatever becomes the season main plot, the two most obvious would be either she's the 'big bad' (which is a strong chance, and villains plans involving either risking their own lives or pretending to be at risk when in reality being the one giving the order is a reasonably fairly common trope), or Lex really is trying to kill her. A lesser obvious, but possible, is they're taking a page from Smllville and gonna have Lex's dad show up and trying to control or kill his family. But having her on the show is something they are likely aware will anger fans if it doesn't lead to a Luthor main villain.

Someone ever tries to kill you... you try to kill em right back.