Supergirl's basic formula since trading CBS for The CW has been to affect the rhythms of a pre-superheroic CW "Millennial working girl" show where the career in question happens to be being Supergirl. That split focus has allowed the series to carve out a tonal niche that sets it apart from the rest of the networks DC Extended Universe offerings, i.e. one where alien invasions or rampaging supercriminals are often positioned as distractions from the "real story" of a domestic argument, an impending date or family drama instead of the other way around: A shape-shifting White Martian can trap everyone inside DEO headquarters, but the most pressing anxiety is whether or not Kara & Friends will get it handled in time to not spoil Maggie and Alex's romantic concert date (they don't, but it's okay anyway because everyone on Supergirl is emotionally twelve years old until they aren't.)
Thusly, whenever the civilian/superhero storylines cross-over both in terms of narrative but also dramatic importance, it's almost always a sign that the kryptonite has hit the fan. So it is in last night's episode, "Homecoming," where that level of cross-narrative impact can't help but be avoided in as much as it involves Kara's family and work life being completely upended by the surprise rescue of her adoptive father Jeremiah Danvers (Dean Cain, formerly of Lois & Clark) from season 2 supervillain club CADMUS. As predicted by a sizable plurality of the series' fans, the obligatory good vibes were short lived: Jeremiah turned out to be seemingly aligned with CADMUS and acting as part of an elaborate ruse - seemingly leaving things off in a state of uncertainty by revealing himself as yet another superhuman enemy for Kara's surprising diverse collection of "Enemies Who Are/Look Like People I Know."
And yet, since there are still 8 more episodes to go for season 2, we still don't know exactly where Jeremiah falls on Supergirl's good/evil spectrum. Or, for that matter, what his endgame is otherwise.
For those in need of a brief refresher: Kara was sent to Earth from Krypton as a tween to act as a guardian for her baby cousin Kal-el, but owing to a fluke of space-travel she arrived (un-aged) about two decades late with Kal having already grown up into Clark Kent/Superman. To help conceal her identity, she was adopted by the Danvers - a husband and wife team of alien-specialist scientists (played by Cain and former Supergirl: The Movie actress Helen Slater) with a similar-aged daughter of their own, Alex. Several years later, Jeremiah went missing (and was presumed dead) after preventing rogue government agent Hank Henshaw from killing Martian Manhunter J'onn J'onzz , who took over Henshaw's identity and worked with the alien-monitoring DEO as secret mentor to Alex and eventually Kara/Supergirl - who in turn most-recently discovered that Jeremiah was alive as a prisoner of CADMUS, a hate group led by Lillian Luthor (Lex's mom) aiming to expel alien immigrants from Earth.
As "Homecoming" opens, Supergirl handily busts up a CADMUS convoy only to discover that its payload was her adoptive father. Though everyone is happy to see him alive (though sporting a permanently-damaged arm), Mon-El is immediately suspicious because it coincides too neatly with the revelation that CADMUS is looking to set off a nuclear device of a type that only Jeremiah himself is capable of helping them disarm. But though relationships are momentarily strained, it turns out Kara's newly-official boyfriend made the right call: Jeremiah is indeed aligned with CADMUS, who've outfitted him with a super-strong cyborg arm (and a brain somehow impervious to Jonzz's psychic probing) in order to infiltrate the DEO and steal their master list of every alien immigrant living (openly or in hiding) on Earth for purposes which - judging by the teases for next week's episode - appear to be straight-up genocidal.
So he's very much working with the bad guys. But is he 100% onboard with their agenda? That seems to be less clear. Dialogue between Jeremiah and Alex leans on the "it's complicated" side of things, and a subsequent exchange with Lilian Luthor implies that they've struck a "deal" of some kind. Granted, if it were easy to figure out what's going on just from these details, Supergirl wouldn't really be doing its job of building up mysteries to be solved week to week - but with the information at hand, a few possibilities emerge.
It's clear enough that whatever is going on is, at least broadly, centered on the alien immigration storylines. Supergirl staked out immigration and refugee issues to be Season 2's "topical" thematic center in much the same way that Season 1 focused on the intergenerational feminist divide between "Millennial falcon" Kara and "lean-in" corporate queenpin Cat Grant; and that focus has only seemed to intensify in the wake of the election of new U.S. President Donald Trump - who's supported policies many consider hostile to real-life immigrant and refugee communities. But the series has balanced out that otherwise unmistakable message by consistently forcing Kara and her allies to grapple with bad guys whose motives aren't entirely evil - and it's hard to imagine that the dizzying amount of bait-and-switch plotting built into the CADMUS storyline not being deliberately set up to induce a similarly "morally complicated" final conflict as the series now sprints to its season finale.
For one thing, there's the matter of Lynda Carter's President Marsden; whose staunch alien amnesty policies helped spur Supergirl into activism and drew CADMUS out of the shadows in the season premiere. While still an "ally" to the good guys as far as anyone knows, audiences (but not the characters) were made privy to the knowledge that Marsden is herself an alien in disguise - so what here broader agenda actually entails is anyone's guess. It's entirely plausible (to say nothing of being "in line" with Supergirl's by now reliable plotting structure) that while CADMUS' outlook is bigoted and their methods genocidal, they may have become so based on foreknowledge of an actual alien threat... one that hasn't fully revealed itself yet and could conceivably involve Marsden. In that context, it's not hard to imagine that Jeremiah has made some kind of "bad versus worse" deal based on the same data: "I'll help you thwart this threat even if it means using your evil methods, just protect and/or don't hurt my family in the process" - something like that.
If that is the case, it's a fair bet that whatever "surprise second villain-threat" is coming is connected to Mon-El. That he's not who he claims to be (a bodyguard to the Daxam royal family who was saved and made able to flee the collapsing world by his friend the prince) has been Supergirl's worst kept secret outside of Alex's previously-latent crush on Maggie Sawyer; and recent alien encounters where would-be assailants declared him "not to be harmed" (but also followed) have yielded a popular fan theory: He's actually the Prince of Daxam himself, and his story about the circumstances of his survival is probably embellished, too. Now, in "Homecoming," his initial (private) confrontation with Jeremiah yielded as a response of "I know who you are - and I doubt Kara would like the truth." So, at the very least, he and CADMUS know what's up with the last(?) Daxamite.
At least one possibility: Mon-El has insisted that Daxam was destroyed by the shockwaves from the explosion of nearby Krypton, but there's nothing to indicate he's being any more truthful about that than his own identity. We've also been informed by Agent Wynn's new alien girlfriend that her similarly nearby homeworld of Starhaven was invaded and destroyed in a fairly recent timeframe. Maybe Daxam actually fell to that same invasion, and said invaders are now chasing the prince to Earth? There's enough room for nearly all of this to be on the table - and whatever goes down it seems clear Supergirl's erstwhile father figure is going to be involved one way or another.