Picture this.
Leviathan takes Lena to hurt Lex once they find out Lex is targeting them. Lena cleverly escapes (because she’s a badass) before getting caught by Leviathan during her escape and ends up being in real danger.
As soon as Kara finds out Lena is in danger, she freakin flies over and beats the crap out of whatever member of Leviathan is threatening Lena, but gets hurt during her blind rage fight and Lena finishes them off and helps hurt Kara. Thus begins their first step towards mending their relationship. Fighting to protect each other and realizing they still care deeply for each other.