One of the main points of the fanfic is to deconstruct Starfleet Magic. Hell, every chapter opens with a Mykan quote that is deconstructed to death. Except the final battle with Celesto, which has no quote to show the seriousness of the situation. Once Celesto is dead, the quotes are replaced with actually heroic ones, reconstructed.
- Starfleet's Protagonist-Centered Morality is deconstructed. Hardly any of the characters, including members of Starfleet find any of Starfleet's actions "heroic". Not to mention the fact that hardly anyone tolerates their Fantastic Racism with both heroes and villains telling the Unicornicopians that they should not underestimate the Equestrians.
- The Unicornicopians' supposed "superiority" is deconstructed as several characters point out that, for a "superior race", they do little (if at all) to prove it. All their self-proclaimed superiority does is get other races pissed off at them for their Fantastic Racism.
- One of the things this fic deconstructs is the marriage between Princess Celestia and Grand Ruler Celesto seen in Starfleet Magic. With Celestia acting more like her canon self, it is shown that the marriage is plagued with several problems, with the two constantly arguing about how Celesto is turning the country into more of a stratocracy and their differing views on friendship.
- Another thing deconstructed is what would happen in the aftermath of United Equestria's creation. As presented, because of how Grand Ruler runs things, Princess Luna is planning to perform a coup on him due to his fascistic leadership; under which includes having re-education camps, "correctional" facilities and censorship of the news just to name a few things going on under his watch.
- The arrival of the Unicornicopians is also deconstructed, with several characters noting that Celesto and Unicornicopia essentially invaded Equestria and forced its citizens to adopt their lifestyle. Because of this, there are high tensions between the Equestrians and Unicornicopians, not helped by the Unicornicopians' "we're better than you" attitudes.
- Lightning and Starla's relationship is taken apart. Starla herself realizes that she's little more than a Satellite Love Interest. After Lightning has his Heel Realization, they agree to divorce and move on to healthier relationships.
- Celesto is also deconstructed in this fanfic. Instead of the wise and noble ruler he (allegedly) is in Starfleet Magic, he is actually shown to be a racist, tyrannical despot who's deeply unpopular with many of his citizens. Also, he is presented to be incredibly closed-minded and having a deep case of Black-and-White Insanity.
- It is also demonstrated that he is terrified of change, which is only creating more problems for United Equestria as the villains themselves know how to counter the tactics he stubbornly clings to despite evidence they no longer work.
- The effectiveness of Starfleet is also taken apart in the story. As it's shown, Starfleet is only effective when fighting enemies like Titan, Fratello, and the Dark King due to all of them using the same Monster of the Week format (and even then Starfleet only succeeds through whatever out of nowhere power or contrivance that defeats the villain). Unfortunately for them, this kind of strategy completely falls apart against Dark Conquest, who knows exactly how they operate, and this fic does not hand out miraculous, out-of-nowhere saves. To wit:
- Starfleet relies on its shields to protect its citizens until they arrive on the scene, with absolutely no active defenses to back them up. This completely falls apart when the villains show they know how to disable them and, as a result, they can slaughter the majority of an invaded city's population before Starfleet even arrives.
- Also, because of their utter dependence on the shields and being told to leave the problems to Starfleet, the citizens are unable to protect themselves once the shields fail.
- Starfleet's inflexibility is also taken apart. So far, Starfleet has lost members, towns, and citizens because they continue to use the same tactics against Dark Conquest, who, unlike the previous foes they've faced off against, sends in small battalions of his troops into cities, which has lead to widespread decimation.
- Starfleet only knows how to fight against one type of enemy: a singular Monster of the Week that, when defeated, causes the bad guys to back off, which are basically the only kind they deal with in canon. Conquest, naturally, stays away from this tactic, and Starfleet's only fallback is to go Straight for the Commander in hopes that the army will rout after their generals go down. Unfortunately, this also fails miserably since they're able to hold their own and don't hesitate to fight with backup, pointedly averting Mook Chivalry. Starfleet thus never stands a chance and is taken out easily while leaving the rest of the army free to run roughshod over the target city.
- Also taken apart is the complete dependence of Lightning Dawn's team on him. When fighting off against a Monster of the Week, the team often acts as the scouts and leave Lightning Dawn to do most of the dirty work. This strategy is proven ineffective when fighting against Dark Conquest's army since they are not fighting one, but many enemies. More often than not, they have to rely on outside assistance to survive.
- Another deconstruction comes in the dynamic of Lightning's team. As it becomes clear that things are going horribly sour and that Lightning does not really know or care about his teammates on a personal level (and thus is unable to cooperate well with them), most of the team has either been killed or decided to bail. Not helped by Grand Ruler's idea of replacing them with random conscripts, which as the Mane Five note, practically dooms them to be Cannon Fodder, which is what happens.
- A lot of the time in Starfleet Magic, Lightning's crew just happens to be nearby when the villains strike, allowing them to respond quickly before the villains do too much damage. Here, Dark Conquest's army deliberately attacks cities where Starfleet is not located, meaning that by the time Starfleet joins the fray, it's already too late, and Conquest's army then proceeds to kick their asses just to rub salt in the wound. It does not help that Grand Ruler refuses to accept that there's a pattern to the enemy's attacks, meaning that Starfleet is never in the right place at the right time.
- Starfleet's "always defend, never attack" mentality, and by extension, their tendency to wait for the bad guys to come to them, get torn to shreds. While it works against the incompetent, clichéd villains in Starfleet Magic proper by fending off their attacks and bleeding out their resources, Dark Conquest actually knows how to take advantage of the fact that Starfleet spends most of their time blundering around in the dark to hit them where it hurts. This results in United Equestria continuously losing ground that they're unable/unwilling to retake, and it's only when Belle actually deciphers Conquest's strategy that the ponies start holding the line.
- Starfleet loves declaring their move names every time they attack. As you might expect, leaving yourself defenseless while telegraphing your attacks so much gives the enemy a prime opportunity to forcefully interrupt. Their initial losses can often be chalked up to them not being able to attack at all since their enemies never give them any breathing room. As shown in the end by Twilight, to call your attacks, you must make absolutely sure you have breathing room first.
- Krysta's entire character gets deconstructed over the course of the story. In the Starfleet Magic fics, she pretty much only exists to get the team from A to B, rarely contributes significantly to a fight, got herself captured on several occasions in the early series, and generally gets shafted later on despite being the main character's best friend. While in canon, she doesn't react to any of this, in Fall of Starfleet, she genuinely believes she's unable to make a difference, isn't valued by Starfleet, and her friendship with Lightning is falling apart, and it's hinted that she suffers from depression as a result.
- The author also deconstructs Rhymey's relationship with Fluttershy: he used a Stupidity-Inducing Attack on her during their first meeting, and Rhymey says outright that he had Mind Raped Fluttershy just to make sure she fell in love with him. Furthermore, he thinks he does everything out of love, but Fluttershy yells at him that he never loved anyone and he ends up losing the sympathy of even his mother.
- The common plot point in Mykan's fics of a hero turning evil because he didn't get the girl also is deconstructed, by showing that no sane person would sympathize with such an entitled psychopath, and that he can be a hindrance even to a manipulative superior, as Grand Ruler himself calls Rhymey out for his obsession ruining both of them, mostly Rhymey himself.
- Chapter 16 deconstructs the practicality of the Uniforce by capitalizing on its biggest weakness: it can only be used once before the user becomes exhausted. After Raven tries to use the Uniforce on Rhymey and Fluttershy, Rainbow Dash manages to save them from the energy blast and Raven is too tired to do anything as Rainbow Speed Blitzes her.
- The (lack of) effectiveness of the lower grunts in Starfleet is taken apart in Chapter 17 with Titan pointing out to Lightning Dawn that the grunts always lose because they are meant to lose so the main members of Starfleet look good as they defeat the Monster of the Week. Thus, while they may valiantly try, the lower members are always doomed to lose. It also makes them even less effective at dealing with Conquest's actually competent army, as Starfleet can only be in one place at a time; without competent backup, they have no way to contain large-scale assaults.
- Fall of Starfleet Side Story: Evolution of Friendship takes apart Celesto Grandruler somehow going from a simple farmboy to retired billionaire astronaut with several characters pointing out how suspicious all this is. And sure enough, it seems Celesto has made some sort of Deal with the Devil in exchange for his current status.
- Sunset and Human Artie's relationship is deconstructed with Sunset pointing out that while Artie has comforted her while she was depressed, they have nothing between them that can lead to a lasting relationship.
- Chapter 3 of Evolution of Friendship shows the consequences of the Starfleet Humans using their superpowers to outperform everyone else in their class when they go through an obstacle course in gym. The teacher, Gray Son, catches them and points out that them using their powers makes the other students, the ones without powers, put themselves down. Additionally, Gray Son makes Starfleet Humans do exercises without the aid of their powers.
