Perhaps fans should have seen that coming when characters were openly wondering where the Man of Steel was during the actual invasion earlier in the episode since Supergirl generally avoids mentioning that there's another more powerful Kryptonian out there who could presumably tip the scales in Kara's favor every time they're momentarily not. Either way, this is about as bad as it gets in terms of stakes for Supergirl - having to fight off her own cousin, who happens to be literally the most powerful being in their known universe.
But that begs the question: how, exactly, did Rhea bring Kal-El under her power? She's fairly strong, but he's stronger, and he's presumably fended off threats of her type before. There also weren't any of the usual "something isn't right here" signifiers that would typically indicate that someone was compromised on this particular series - no glowing eyes, no weird pieces of technology stuck to his head or chest - suggesting that something new or at least more obscure is at play. What could be going on? Here are a few possibilities:
In screenwriting, there's a maxim called "Chekov's Gun" that goes like this: If a gun is mentioned in Act I, it will be fired by Act III - basically, everything in a movie (or play, or really any properly-constructed narrative presentation) is there for a reason, so if it's coming down to the wire and you don't know how a story-point will be resolved, start thinking about any guns that haven't been fired.
Thus far, the Chekov's Gun of this whole storyline are the supposedly vast stores of Kryptonite and Kryptonite-based weapons supposedly being carted around by Rhea's mothership. Thus far, she's only showed off a handful of bladed Krpytonite melee weapons, so presumably, there must be a few more. While we're all most familiar with the classical green variety that temporarily de-powers Superman (and Supergirl), it has actually come in several different colors in the history of Superman lore - and they all have different effects. For example: Red Kryptonite (which Supergirl encounters in Season 1) turns good guys into bad guys. Orange gives powers to animals. Gold shuts off super-powers permanently. Blue can hurt Bizarros. Pink... well, it's best not to dwell on what Pink Kryptonite does.
There are also several varieties that have been known to alter a Kryptonian's personality: Black Kryptonite once split Superman into good and evil halves, Periwinkle (yes, really) takes away his inhibitions and Silver is something like a psychotropic drug. The uses and origins of all these different types has been pretty malleable over the decades, so it's not outside the realm of possibility that Rhea has acquired (or developed) some variety that would turn him into a temporary pawn.
Something Season 2 has leaned on pretty heavily for handwaving storyline issues is the idea that Kryptonians and Daxamites are remarkably similar on the biological level, meaning that what's true for one tends to be true for the other. Rhea has deployed a mind-controlling henchman in a bid to manipulate Mon-El at least once before, so it's reasonable to consider that something similar could be at play for Superman here; especially since (at least in traditional Superman canon) he's as susceptible to mind-control as any other being under most circumstances - though some storylines have featured him learning specific techniques to guard against the same.
Either way, mind control is a fairly common power both on Supergirl and in the broader "Arrowverse," so the idea of some not-previously-encountered technology (or alien species) being revealed as behind Superman's manipulation wouldn't be a far reach for a series where function tends to follow form when it comes to making up new fake science.
It's Not Really Him
It's the Season Finale, which means it's expected for all of the series regulars and semi-regulars to turn up and affirm whether or not they'll be around for Season 3. You know who we haven't heard from in awhile? Miss Martian. Last seen heading back to Mars to take the fight back to the rest of the White Martians, she's been expected to turn up at some point in the finale but has yet to appear... or has she?
Remember, she's a shape-shifter whose proven susceptible to control or manipulation by more powerful enemies before - along with proving herself a physical match for Kara in one-on-one combat. Using her (or, really, any of the White Martians, who all have the same shape-changing abilities) in the form of Superman would be a clever piece of psychological warfare - though it would beg the question of where the actual Superman actually has been all this time.
Whatever is going on, fighting even an approximation of Superman is undoubtedly a complication that Supergirl wasn't counting on - and what the effect on the season finale will ultimately be remains to be seen.