Phantom Zone AU where Lena uses an exosuit and a transmat portal to go to the PZ and find Kara. Her tech gets her pretty close to Kara, actually, but between the short search and the inevitable fight with some wraiths/resentful PZ residents, they're there for what feels like maaaaybe a few days. Which are long enough, but even so, by the time they tumble back through the portal back to Earth, they discover that time in the PZ passes differently than on Earth.
Because it's been several years since Lena left.
Maybe the Tower isn't even the Superfriends' base of operations anymore. Maybe they step through the portal into a residence housing a bunch of college kids. Maybe Lex found the Tower and destroyed it, having turned the public against them and other vigilantes/aliens.
Either way, nothing is the same.
While Lex had announced his fear and concern about Lena and Kara's absences to the public, he had privately claimed responsibility for Lena's disappearance, taunting them that he had killed her (maybe Lena had left a bit of mess behind her when she left, which had supported his claims-- along with the fact that Lena couldn't possible be stupid enough to go into the PZ alone so it doesn't even occur to them that she would).
So they believe Lena dead, and with their best chance of getting Kara back 6ft under, they believed Kara lost for good.
Which means Kara finds her sister barely holding it together, broken up with Kelly and her plans for a family up in flames.
J'onn isn't faring much better, for having lost yet another daughter and been unable to help the one girl he has left.
Nia and Brainy have broken up, but are faring better than J'onn and Alex.
Andrea has joined the Superfriends as Acrata in a bid to exact revenge on Lex for killing Lena. She's the only one whose anguish is focused on Lena instead of Kara. (Most of the others simply count Lena as a victim of Kara being gone, the first of so many that they've become numb to it all.)
All of this leads to Kara and Lena having to work together to put it all right. Kara focuses on helping the aliens and others dispossessed by the smiling stranglehold Lex has on the city, while also trying to salvage what's left of her sister.
Lena focuses on Lex directly, as she's the only one who stands a chance in squaring off with him directly, both physically and intellectually. And she's wildly successful, considering that Lex has no idea she's back and blames Acrata for his private journals going missing and his manipulative treatment of Lena while growing up making a splash on the front page news.
Lena upgrades her exosuit to exceed Lex's, so when she and Kara finally reveal themselves, they're well matched. It's still a tough battle, but Lex's lack of concern for collateral damage not only puts Lena and Kara at a disadvantage as they try to mitigate his recklessness, but also cements his villainy in the public's eye, as both news crews and cellphones capture footage of his rampage.
When he's defeated-- with Lena walking away after deciding not to kill, only to have Kara incinerate him with her heat vision when Lex when he tries to shoot Lena in the back-- they're the two who are left to pick up the pieces.
Lena takes over at LuthorCorp again (which soon becomes L-Corp, as it should be), and Kara works with the disenfranchised to rebuild and accommodate alien/disabled needs. It takes years, but they succeed in returning National City to its rightful place as a beacon of hope and acceptance in the world.
This time, when the next statue of Supergirl is erected, Lena is cast in bronze right beside her.
