“Alex and Kara (Melissa Benoist) have a little misunderstanding, actually,” showrunner Andrew Kreisberg tells TVLine. “She thinks Kara might not be OK with it.”
Indeed, Alex will sense a “sadness” in her sister after sharing her bit of self-discovery, the EP says — though it’s not born of any disapproval (“Kara doesn’t have an ounce of prejudice in her”

, but guilt.“Kara feels like their entire childhood was relegated to worrying about keeping Kara’s [alien] secret, so she feels awful that, maybe if she hadn’t come along, Alex would have been able to reconcile this aspect of herself sooner,” Kreisberg explains.
But once all is said and done, Alex’s journey will only strengthen the sisters’ connection, to be sure.
“All this does is make them love each other more, which is something that was really important to us,” Kreisberg shares. “As people will find out this season, everybody treats Alex with the love and respect that she deserves.”