SUPERGIRL at the end of Season 2 and the start of Season 3 is having a few collisions with reality. SUPERGIRL seems to have no sense of how the US military works and also has no sense of how federal security and counterintelligence agencies would handle a human resource crisis. SUPERGIRL also seems oddly unaware of how big planet Earth is.
Season 2 of SUPERGIRL has a finale that seems to collide with the reality of how the United States would actually respond to an alien invasion and the reality of SUPERGIRL's cable budget. Season 2's finale has the US President fighting aliens on the frontlines and Lena Luthor dosing planet Earth's atmosphere with an anti-Daxamaite poison using a single desktop device that's smaller than a fish tank.
Season 2's finale was, despite some peculiar storytelling choices in military strategy and technological scale, emotionally resonant. All the character arcs are spectacular: Kara can save the world, but she has to render Earth uninhabitable for the love of her life, Mon-El; she has to put him back in his Kryptonian lifepod and launch him away from Earth. The contrivances to reduce a global alien invasion to being confined to National City were... contrived. However, the contrivances were to serve a low budget and also for character beats that made sense emotionally even if the plot itself didn't always make sense.
One has to wonder why the writers weren't finding a more sensible reason to have President Marsdin present in National City than having Marsdin nonsensically leading the US Air Force into battle with the unarmed Air Force One -- such as Marsdin having deliberately ensured being in town to prep DEO defenses against the Daxamite invasion she'd been expecting.
One wonders why the writers didn't establish that putting low level amounts of lead throughout Earth's atmosphere was going to be accomplished with a global network of satellites venting exhaust and that Lena's thermos-sized machine was to link and activate the satellites, not to accomplish the entire planet-sized job from Lena's desk.
Season 1 was very capable in reducing SUPERGIRL's plots to the budget at hand. The Season 1 finale came up with reasons for why the Kryptonian soldiers were reduced to two. The Season 1 finale presented the Kryptonian attack on Earth as a psychic weapon that could be rendered with actors performing headaches so that pyrotechnics weren't needed. SUPERGIRL was good at building ramps over potholes of plot to justify scenes that would otherwise be irrational.
Why did these skills seem to desert SUPERGIRL in Season 2?
It seems to me the problem is the presence of unrepentant sexual harasser Andrew Kreisberg, the showrunner for SUPERGIRL, and the absence of Ali Adler, the original lead writer. Season 1 of SUPERGIRL had its scripts led and overseen by the brilliant Adler (CHUCK, GLEE, NO ORDINARY FAMILY, FAMILY GUY) who had a lot of experience in managing stories to fit low sitcom budgets. But Kreisberg had been sexually harassing and verbally abusing his staff, including Adler. Adler reported Kreisberg to human resources and her complaint didn't move forward. Adler quit SUPERGIRL. I've heard that as of the filming of Season 2, Episode 8, Adler refused to spend another moment on SUPERGIRL and moved into a CBS development deal, taking her away from the CW, from SUPERGIRL and from Kreisberg.
Adler retained an executive producer credit on Season 2 and it seems that her story outlines remained, but Kreisberg took over fleshing them out into full scripts. The stunning Episode 15 would appear to be the finale for Ali Adler's writing on the show.
Adler's story ideas took SUPERGIRL to the end of Season 2, but Adler wasn't shepherding her stories from outlines to scripting to filming. As a result, the Season 2 two part finale seems to feature Adler's emotional points (the President revealed as an alien, Kara having to rescue Lena and Mon-El from the spaceship that Alex has to destroy, fighting a mind-controlled Superman, Kara sacrificing her life with Mon-El to save Earth) -- but not Adler's ability to plot the connective material between the big setpieces and emotional conflicts.
Thanks to the characterization, Season 2 feels like a success, but that success is on some very shaky writing. Kreisberg clearly recognized the value of Adler's character beats, but he also clearly didn't have the skill to move the story from A to B without a lot of clumsiness along the way.
That clumsiness also seems present as we go into the Adlerless Season 3 of SUPERGIRL: Season 3's first two episodes show Kara to be absolutely traumatized by Mon-El's loss. Kara keeps flashing back to her mother (now played by Erica Durance and it's great to see her). Kara keeps remembering the terror and helplessness when she was 12 and stuffed into a metal tube that was shot into orbit while her planet exploded behind her.
Kara is consumed with guilt that she's now done the same thing to Mon-El, sending him off to dangers unknown. Melissa Benoist's performance is painful to watch.
Kara is coldly unresponsive to the civilians she saves as Supergirl, blank and unable to meet her deadlines as a reporter. Kara is avoiding her friends, cancelling every outing with Lena Luthor and avoiding the weekly game night. When Jimmy, now Kara's supervisor at Catco, reminds Kara to meet her deadlines, Kara is volatile and aggressive. When Alex asks Kara to connect with her friends and sister, Kara is abrasive and declares that Kara Danvers is a failed experiment and that attempting to live a human life has been a mistake.
It's a very strong character arc where Kara's unprofessionalism at Catco continues after best friend Lena Luthor buys the company. Lena sweetly suggests that Kara take a leave of absence to deal with her grief over Mon-El (whom the world knows was dating Kara, not Supergirl). Kara lashes out at Lena and snarls at Lena to only speak to Kara about work and not personal matters; Lena agrees and informs Kara: Kara is missing meetings. Kara is treating work orders from her employer as an inconvenience. Kara's behaviour at work is unacceptable.
Kara softly says she'll get to work on Lena's assignment. Later, Kara apologizes to Lena, thanking her for being a great friend and a great employer, and Kara recognizes that something inside her is fundamentally broken that has to be addressed.
SUPERGIRL's Season 3 character arc is fine. Kreisberg is solid with characterization. But the plot makes no sense. Kara Danvers is an employee of the Department of Extranormal Operations, a federal emergency response bureau. Kara Danvers just fought in a war. Kara Danvers is on active duty. Kara is a federal employee with the highest levels of federal security clearance; there is no way that the DEO would not be putting her in mandatory psychotherapy after Season 2 for survivor's guilt (she thinks Mon-El is dead), for combat trauma (she had to fight Superman) and for grief.
I understand that two episodes of Kara lying on the psychoanalyst's couch would not be the greatest use of Supergirl and her superpowers. But it's ridiculous to think that J'onn J'onzz, a federal emergency response manager, would allow Kara's trauma to go untreated. Or that Alex Danvers, a medical doctor (license unacquired), would leave Kara to deal with all these serious mental health issues on her own. Or that President Marsdin would allow a trauma victim with superpowers to keep working in a high securlity clearance government role without counselling sessions.
Once again, the issue here is rationalization to justify the more irrational story points. Adler would have understood that Kara would be seeing a DEO therapist; Adler would have found a way to have the therapist report that Kara was not a danger to anyone but deeply depressed over issues that Kara wasn't willing or able to verbalize, enabling the story to proceed with Kara trying to manage her grief alone.
Kreisberg seems rather dismissive of mental health care in real life and on his shows. And in a fictional context, it made sense that Oliver Queen wasn't seeing a therapist because he had a secret identity to protect. Barry Allen also had a similar situation. But Kara Danvers was working for the federal government as a secret agent and her sister was a physician (albeit having never been licensed).
It makes no sense that psychotherapy is never even discussed, and it speaks to Kreisberg's mindset where psychological problems are to be addressed with force and catharsis in the course of dominating life's problems rather than seeing a doctor.
It's noticeable that in Season 4, SUPERGIRL introduces a psychotherapist and neurologist in the Kelly Olsen character -- a development that could only happen after Andrew Kreisberg had been fired off the Arrowverse the previous year.