The story of a JPRG is one of its most important elements, even more so than most game genres, so let's start there. First we'll look at the plot overall, and later at the individual characters.
So what is this game about? Final Fantasy IX starts out as a story about a cocky rogue, a runaway princess, a lonely kid, and an uptight knight trying to make sense of a war started by their own country that threatens to engulf the whole world as they know it, that being their home continent. They acquire new allies, learn uncomfortable truths about themselves and their homes, and travel beyond every border they've ever known to try and stop this senseless destruction, all while romance blossoms between the rogue and the princess.
This makes for a compelling story that can be understood on a personal level and scope, but it ends by Disc 2. Disc 3 opens with Zidane being uncharacteristically angsty, followed by the destruction of Alexandria, which catapults the narrative into a world-wide stage, even though there's barely anything else to the rest of the world, and then into inter-planetary nonsense that quickly starts breaking too far away from the game's more traditional fantasy with a hint of steampunk aesthetic. By the time the game gets to Terra, interest starts to wane because the game has moved beyond both its own established setting and scale, and has left half the characters by the wayside. By Disc 3, only Zidane, Garnet, Vivi, and Eiko still matter to the plot; everyone else is coincidental, even taking Steiner's romantic subplot with Beatrix into account.
This is a problem hardly unique to Final Fantasy IX; it plagued a lot of games and anime alike from the 90s and 00s, and it's not hard to see why IX went in this direction, after both VII and VIII upped the ante to the destruction of the planet and the destruction of time, respectively. Destroying both in IX must have seemed like the logical next step in the series' progression, but IX was a throwback to earlier games in the series in many respects of its aesthetic. It would have made perfect sense for it also to be a throwback in terms of the ultimate villain's scope, making it something of a Breather Level for the entire series, and allowing future games to also tone their narratives back down to more manageable levels.
IX's story was at its best when it was about the war threatening the Mist Continent, and creeping into the Outer Continent. Every character had a direct interest in the war (except for Quina, but we'll come back to that), and the scope of the threat was human. It was on a level the player could easily comprehend and internalize in a way that a 5000 year metaphysical interplanetary collision just isn't. Considering how largely unused the other two continents of Gaia were, it would have been easy to move the Terrans onto one of them, thereby cutting the second planet and the misplaced high technology out of the mix. The Terran's backstory and motivations wouldn't have to change much to accommodate this, but it would make the narrative's scale much more comprehensible, and therefore more engaging.
Beyond reaching an unrelatable scope, the narrative also takes a turn for the incomprehensible during Discs 3 and 4. Character's reasoning or motivations might sometimes be suspect during the first two discs, but it the story was very easy to follow: something nefarious and mysterious is going on in Alexandria, leading it to starting wars with its neighbors to acquire magic crystals in order to... wait, why did they want the crystals? All the eidolons Brahne summoned were ones she extracted from Garnet, so what were the crystals for? Since they originally contained a super eidolon that was too powerful for the summoners to control, maybe Kuja wanted to claim that eidolon in order to fight Garland, but it seemed like Alexander was his target all along, and once all four crystals came into the party's possession, they never did anything with them again.
So yeah, there were some serious inconsistencies in this plot throughout. Still though, it wasn't until Garland just couldn't get the story straight that things started getting really noticeably inconsistent, to the point that translation errors seem a likely culprit. It didn't help that Garland was a exposition dumper, which made it all the more irritating when it was impossible to follow what he was rambling about, especially when finding out that the black mage plotline the game already devoted so much time to is being repeated with the Genomes is so fresh in the mind. It ultimately pays off, but it's still an eyerolling moment.
The plot does come back together in the end, though. Kuja taking back the reins as the focus of the narrative at the end of the Terra segment helps get the game back on a track the player can understand without metaphysical nonsense, and his shift in motivations when he learns that he, too, is nearing the end of his lifespan results in a solid payoff to the running theme of existentialism that's been going throughout the game when it's shown how he and Zidane come to different reactions to the knowledge of their mortality, and their ultimate reconciliation on the former's deathbed. Still, all that could have been accomplished without the need for a second planet.
IX's main plot is solid for the first two thirds, takes a major dive in the third, but recovers by the end. It suffers from holes in characters' reasoning and motivations, inconsistencies ranging from minor to major, incomprehensible metaphysical nonsense in the later acts, and drops half the cast into the background halfway through the game. The story could have been much stronger if it had cut the interplanetary doom plot and stuck more closely to its originally established medieval war/steampunk-renaissance setting, keeping the scale smaller and more personal to both the player and the characters; but despite its flaws, it's mostly enjoyable, and the ending pays off for every major character to one degree or another.
Plot Rating: 6.5/10
