* AlternateCharacterInterpretation: Just how truly evil Destoroyah himself really is? While Destoroyah is near universally considered one of the most violent kaiju in the franchise, the reason behind the violence is left vague. Some think that it's simply a case of Destoroyah being a genuine sadist and taking pleasure in the devastation he causes. Others interpret his actions as a NonMaliciousMonster that is acting on instinct, and lashing out at everyone after him/they had been harmed to remove threats to himself.
** For starters, it is Junior who attacks Destoroyah first and causes the whole battle to escalate. Also, once a dying Godzilla uses the Spiral atomic breath on Destoroyah, leaving him coughing up blood and mortally wounded, Destoroyah actively attempts to [[ScrewThisImOuttaHere flee the scene]], only to have his wings frozen solid by the military, causing him to fall down to the ground and die for once. On the other hand, his micro form actively targets the fishes in the aquarium and he also appears to laugh sadistically while fighting Godzilla.
* AwesomeMusic: ''Godzilla vs. Destoroyah'' features the last all-new soundtrack by Akira Ifukube before his death in 2006, and has some seriously chilling pieces in it. Special props go to Destoroyah and the Super X3's themes.
* CreepyAwesome: Destoroyah is one the purest examples of NightmareFuel in the franchise, and the fans love him for it.
* CrowningMomentOfHeartwarming: After a TearJerker conga at the end, we see that Junior absorbed his father's radiation (saving the world in the process) and has matured into a fully grown adult as the next Godzilla. Our little prince we've seen grow up over the last few movies has taken the throne as the new king. Better yet, due to his upbringing among humans, he'll likely be actively defending humanity a la the Showa series.
* EnsembleDarkhorse: Though he's the main villain, as a Kaiju overall, Destroyah has quite a large following thanks to this movie. Many saw him as an insanely dark and cruel monster that gave Godzilla one hell of a show.
** Remember the line "Godzilla never does destroy Japan"? Remember Junior's GentleGiant nature? Now the line has a new meaning due to the mess by the Futurians. The reason why JapanTakesOverTheWorld is maybe due to Junior being a gentle giant in the movie.
** Speaking of ''Film/GodzillaVsKingGhidorah'', that film retroactively foreshadows the end of this one: Junior is killed then later revived and mutated into an adult Godzilla by the fallout of his father's meltdown; much like how the Godzillasaurus in ''Film/GodzillaVsKingGhidorah'' was killed then later revived and mutated into Godzilla by a crashed nuclear submarine.
** Destoroyah was invulnerable to the military freezing weapons after his first OneWingedAngel transformation, but it's ultimately what does him in. Why? Because he'd just been super-heated by Godzilla's meltdown. His super-heated armor was rapidly cooled, subjecting him to thermal shock. He was probably reduced to a fragile wreck before he hit the ground, allowing the impact to finish him. This means that Godzilla ultimately gets the credit for Destoroyah's defeat, even though he didn't deliver a killing blow.
** In the original film, Serizawa tells Ogata to be happy with Emiko when he makes his HeroicSacrifice. In this film, she did not marry him after the events of the original and is most likely suffered from SurvivorGuilt when she felt she had no choice but to reveal the Oxygen Destroyer.
** Serizawa's fears of the Oxygen Destroyer has become a reality now that the Oxygen Destroyer has awaken and mutated Precambrian life-forms whose powers derives from the weapon that killed the first Godzilla.
* MemeticMutation: DESTOROYAH!!! In the Godzillathon review of this movie, James Rolfe always says "DESTOROYAH!" whenever he addresses him. He even does this in the AVGN episode "Godzilla".
* NightmareFuel: The film surprisingly has an amount of nightmare fuel in the film. These include:
** The side-effects of Godzilla melting down. The red on his face and body does not help.
** Destroroyah's unnerving appearance and his roar. Does not help that his final form looks like "the goddamn devil".
** The fact that Destoroyah was awaken by the Oxygen Destroyer meant Serizawa's fears had came true. To the point he stripped several fish to the bone in the aquarium scene.
*** The fact that Destoroyah is the living embodiment of the only weapon to ever permanently kill Godzilla. No last minute radiation, no magic, no nothing, that Godzilla was '''dead'''. And now that weapon is a giant monster. Imagine if the Tsar Bomba gained physical form and started walking around.
** Junior's death, and Godzilla's failed attempt to revive him. The music for this sequence is appropriately titled ''Roar of Sadness'', and is a solemn version of Godzilla Junior's gentle string leitmotif. Also, Godzilla's death.
** Hell, even the events leading up to Godzilla Jr.'s death was a TearJerker when you really think about them. Up until the final battle, Godzilla was desperately in search of his son, following him from location to location. Godzilla apparently ''knew'' he was dying, and like any father on his death bed, wanted to see his son one last time. And just as they're about to embrace, [[KickTheDog Destroyah breaks up the reunion and kills Junior.]] No wonder Godzilla got so pissed and started beating Destroyah so savagely. [[DoNotGoGentle Godzilla had nothing left to lose.]]
** Emiko Yamane post-1954. In the original film, she was one of the witnesses of the original Godzilla. The film heavily implied she is suffering from SurvivorGuilt after what she did: Reveal the Oxygen Destroyer. Not only was she unfaithful to her fiance, but Daisuke told her to be happy with Ogata. But considering her surname, the film also implies she didn't marry Ogata either.
** Godzilla's death is this. Just watching Godzilla, a massive symbol of ''power'', melt into radioactive sludge is just sad. Ifukube's haunting score just hammers home how sad this moment is.
* TheyWastedAPerfectlyGoodPlot: A scene featuring Godzilla giving Destoroyah a NoHoldsBarredBeatdown as dies was removed because it lessened the impact of Godzilla's death, though it's still pretty satisfying to watch. However, that ending was shot as a dupe and never meant to be used. Wires and filming equipment can be seen in many of the shots, betraying its hastily put together nature.