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In Final Fantasy Tactics, every time you meet a bad guy important to the plot and you defeat them, they teleport away at the "last second", despite laying down "knocked out" in battle for the last half-hour or so. You can get the teleport ability but it does have a tendency to fail over long distances, apparently this doesn't apply to them. What's also annoying is that they only die when the plot demands it, there being zero difference between what you did before and what you did to defeat them the second or third time around. Talk about Gameplay and Story Segregation.
It doesn't apply to them. You learn Teleport, but they have Teleport 2. You can actually hack the ability, and it lets you move anywhere on the map without failure rate. Of course, it doesn't explain the characters without Teleport 2 doing this...
In the game you manage to come across one of the twelve or so MacGuffins in the game by defeating a boss, later on the main character gives it to a low-level white mage character for "safe-keeping". Surprise surprise, she gets kidnapped, and the MacGuffin is stolen.
Final Fantasy XI ended up with a whole bunch due to the fact that Square never seemed to divert their best writers to it:
Bastok mission 9-2 (technically part of Rise of the Zilart, but branching off from original content), itself part of a series of plotless backstory exposition on the Galka race, just randomly takes a noble if misunderstood character and derails him into fighting you because the developers needed a big boss battle to end the mission tree.
The character of Prishe in Chains of Promathia pretty much turned what could have been an interesting story about ancient arcane civilizations and turns it into a glorified scavenger hunt for a horribly abrasive character and her fawning entourage. For a description of the character herself, she also has an entry in Tsundere Sue (that, alone, should say quite a bit). A more specific example, though, is mission 7-5, which completely derails one of the characters in order to force a boss battle, then just negates it all without anybody so much as even giving him a second glance.
The quest "Apocalypse Nigh" (which is technically a continuation of the Rise of the Zilart and Chains of Promathia storylines). Obviously borne out of player outrage at the death of a popular character during the primary Zilart storyline, it comes up with a flimsy excuse to bring her back (which is made more dubious considering the character never gets used again). The moment it hits the wall is when you see every major villain in the two storylines take on every major protagonist in what was a very blatant "making it up as we go along" story.
The plot of Treasures of Aht Urhgan hands you the Idiot Ball, putting you through utterly idiotic But Thou Must choices in order to force the plot along.
Time will tell if any consideration is given to the gross negligence towards time paradox situations that the Wings of the Goddess expansion has chosen to ignore for now.
From Final Fantasy VII: after getting the Black Materia back from Jenova, Cloud decides it would be best to let someone else hold on to it in case Sephiroth decides to control Cloud again and gives the one that volunteers strict instructions not to give it to anyone. note While Red XIII is usually the one to be picked to hold it, it is possible to get someone else to do it (including Barret). Later on, said individual is tricked by Sephiroth into coming to the aid of the other members of the party. When he/she arrives, the first thing he/she does is give the Black Materia to Cloud without question, despite earlier instructions, not to mention having first hand knowledge that Sephiroth could manipulate Cloud into getting the materia. Granted, everything more or less works out in the end, but after watching it all unfold you start to wonder if they're worth the trouble.
In the DS remake of Final Fantasy IV, the ancient, very wise character Fusoya gives the party a piece of advice prior to fighting the boss "CPU", advising the party to take out the Defense Node first in order to prevent the boss from being able to heal itself. While this was indeed good advice in previous versions of the game, here it is a surefire way to get the whole party brutally slaughtered since they greatly increased the amount of damage Attack Node does on your party but didn't bother to give Fusoya new advice.
The fact that the Garment Grid in Final Fantasy X-2 works in absolutely every single conceivable way different when Leblanc uses it at the start of the game. When the player uses it, it merely changes your clothes and gives the girls a new weapon and new spells to cast. The most a Garment Grid will ever do when it comes to any physical changes is hair length and a set of minor changes such as paws whilst using the Berserker sphere. Leblanc on the other hand is capable of transforming into an exact duplicate of both Summoner Yuna from the first game and Songstress Yuna despite the problems that: There is no Summoner Dressphere, Yuna no longer looks like that anyway, Leblanc is able to use spells that the Songstress sphere can not, there is no stated ability whatsoever to completely transform your body into someone else, if there is a clone feature why do the girls never use it even though it could have come in handy to break into several places throughout the game and how did she steal two spheres from the Gullwings anyway? Even at Level 1 Leblanc, Logos, Ormi and her Goons are no threat to even the most shockingly awful player imaginable. An almost classic example of both a wallbanger and a Voodoo Shark as probably any explanation to resolve this would probably throw up a whole host of other questions.
The decision to hold the concert in the Thunder Plains AKA an area of land where there is a never ending thunderstorm. As opposed to say... the Calm Lands that are located a slight stroll away from the world's biggest and most important city where there are already flourishing entertainment facilities set up and, you know, isn't constantly pissing down. Or the Blitzball Arena located in the world's second biggest and most important city and where she held her last concert due to the fact that, despite what we're told, this crowd in no way looks like it outnumbers that one.
The resolution of the conflict between New Yevon and the Youth League is completely unrealistic. Yes; Baralai and Nooj have made up and as the leaders some people would certainly listen to them. However the ideological problems that led to the conflict in the first place have not been resolved. The ex-Yevon citizens that form New Yevon still want to return to the old days of Spira's Theocracy. The only possible concession they appear willing to make is to lift some of the machina taboos. The members of the Youth League however want democracy and freedom; free from any and all of Yevon's doctrine. It is absurd to think that a concert and a speech would correct these fundamental differences between the two viewpoints and any coalition government between them would ultimately fall apart because their goals are simply too far removed from one another. What would actually happen in real life is the disgruntled members of Yevon and the League would either oust/ignore Baralai and Nooj or simply start up other groups that are exactly the same in all but name.
Final Fantasy XIII: The fact that the Fal'Cie need l'Cie to complete tasks for them, but they won't tell them what the tasks are, despite imposing a lethal penalty if that task isn't completed in time. Reaches the point of Rage Quit when it's revealed the Fal'Cie can speak English, meaning there's no reason for them not to just tell the l'Cie their Focus in the first place.
Actually, it might be even worse than that! They do give you a clue, but all you get from the Fal'Cie is a hazy mental image without any context, meaning that you still will have no idea what you're supposed to do as a l'Cie in order to avoid being turned into a mechanical zombie. Imagine getting a hazy image of the president. That can basically mean anything from assassinating him, saving his life, giving him a handshake, putting a burning bag of dogturds at the White House, making him sing every song from ACDC, you name it. And considering that the "reward" for completing this near impossible task is to be turned into a giant crystal, it's safe to say you're screwed either way!
The fact that the Purges are completely unnecessary; there's no need to evacuate entire cities, because l'Cie have very clear glowing tattoos that identify them. All you need to do is strip search the populace. (Which is still... problematic... but in a different way)
The introductory sequence which set up a powerful tone using almost Holocaust-esque imagery to present a powerful scenario... treated with an light-hearted action hero tone. Directive misfire indeed!
The heroes' hypocritical murder-rampages; after the game's constant weeping about the protagonists being branded "enemies of Cocoon" and making it out to seem so unfair, Hope, Snow, Lightning and Fang all slaughter dozens upon dozens of officers - who are desperately trying to take them in alive despite the orders of their superiors - and generally terrorize the populace, either by firing guns into crowds or, in Lightning's case, plotting the outright destruction of Cocoon. The supposed "protagonist" nearly staggers towards Sociopathic Hero in various insane ways but the game presents it as tragic.
The fact that Sazh and Vanille do quite literally nothing plot-relevant and wander for at least three levels - the game even admits they're "wandering aimlessly." One of these levels is an amusement park - which is also a wall banger, because there are no sidequests or minigames of any kind, and you can't even ride the chocobos that appear.
After at least three different cutscenes of heroes surviving completely ridiculous crashes at high velocities and absurd heights without a scratch or sign of damage, Snow and Hope fall off a roof - and Hope, even though Snow bear-hugs him through basically the whole fall, ends up unconscious.
The fact that Eidolons - supposedly the "salvation" of l'Cie - actively try to murder their summoners, not to mention the ways to defeat them are fairly counter-intuitive. It seems like the fal'Cie missions are less noble callings and more open invitations to Everything Trying to Kill You.
The extremely brilliant idea of going straight to Hope's house. Going to the house of a known l'Cie... to hide from the people... who are looking for the l'Cie.
The fact that the fal'Cie all look completely different - meaning you can never tell what they are or where to look for them - and seem to have varying levels of sentience.
Lightning's extremely cool gravity warp tool thing - showcased extensively in trailers - is used in two cutscenes in the game's opening hour, once in a fight, and once to stop a fall from a high place (not that it would have hurt them anyway.) It's never used again, in battle or in the story.
Makes sense, since her original one was broken when Sazh clung to her when she wanted to leave during the first Chapter, and the ones used during the later jumped probably were taken from fallen PSICOM people.
The fact that the entire story is borderline incomprehensible unless you read through the data logs... and even then, they don't explain some of the most pressing questions. This one in particular bugged Yahtzee as well, who put it like this:
Yahtzee: You're supposed to weave exposition into the narrative, not hand the audience a fucking glossary on their way into the theatre!
One worse; this game will sometimes do the polar opposite: tell you about things that have no relevance to the plot whatsoever. "Did you know that these ruins on Pulse were once inhabited by people?" (blatant exaggeration, but some datalogs like the Undying are pointless) Yeah. And?
The utter mish-mash of narrative. We're given heroes that spend their time bickering and fighting among each other for the sake of the story, which in and of itself would be harmless, but the plot and over-arching conflict itself doesn't call for a character-driven narrative. The story presents itself as a character driven story, but the story itself is not a character driven story!
And how about that gameplay? They made the exploration, travel, and shopping as non-interactive as possible for the sake of the story, which is already a highly debatable decision when the whole point of a game is to have meaningful input, but is utterly unjustifiable when the story as bad as this one. Next, they make a system which required a three unit offensive playable throughout the main portion of the game with only two people, which makes players feel like they are stuck in a tutorial until chapter 10! OF A THIRTEEN CHAPTER GAME!! Then they make the combat as non-interactive as possible because they figured that players get bored with making the same decisions over and over when level grinding or fighting bosses, so instead of making the battles more interesting (the staggering mechanic was a good start, but not enough), they just let the computer make the boring and sometimes boneheaded decisions for you. Then they top it off by padding out the enemies with ridiculous HP totals, packing it with more tedium than ever. Sure, FFX's exploration was linear, but at least there were interesting branches to the path sometimes, places you were free to poke around on your own, and - love it or hate it - a better story to justify it. And FFXII's combat system was heavily automated, but also heavily customizable to present its own brand of challenge, and allowed for a manual override anytime you wanted.
The fact that our heroes would have literally managed to destroy Cocoon and kill millions of people if it wasn't for Vanille and Fang turning into crystal after the world was already doomed. What makes this a wallbanger and not a conventional Deus ex Machina is that there is absolutely no way whatsoever they knew that was going to happen. The scene shows them visibly shocked at this turn of events as the planet begins plummeting toward the ground in a fireball. Also despite being told by Barty for at least twenty hours of gameplay that the destruction of Cocoon was exactly what was going to happen if they continued on their present course, they apparently didn't discuss even a token plan for the eventuality that he was telling them the truth. For all their posturing that their focus was to save Cocoon, the evidence proves that they would have achieved the exact opposite if it wasn't for sheer unpredictable and random chance.
Hope's mother just outright abandoning her terrified young son in the middle of a war zone despite the fact that not ten seconds ago she remained absolutely silent whilst Snow asked for a volunteer to stay behind with an assault rifle and guard the civilians - where she would have been able to both directly protect her only child and would have allowed her to comfort him in the process. Also no matter how heroic you may think she was being with this decision; one middle-aged and apparently untrained woman was going to make a Hell of a lot more difference as a sentry than she ever would have charging against an army. Crosses neatly with Idiot Plot when you realize that the whole thing was a set-up for the Hope swears revenge storyline.