This is pretty tough. I find it takes several hours to fish out a successful attempt, time that likely would be better spent just gaining enough levels on the Sphere Grid to beat him legitimately. Regardless, I'd seen a lot of chatter about how Dark Yojimbo makes it impossible to do a low level Penance sweep with Zanmato, so I wanted to see for myself. Overall I'd say the difficulty was not exaggerated, but it can be done if you're stubborn enough.
First, I start off from a Save Sphere in the Calm Lands. This is weird and I don't know if it's real or not... but I've read there's a glitch where if you load in at the area around the Cavern of the Stolen Faith, it resets Yojimbo's Compatibility. Again, I can't confirm if this is true, but when I attempted to do this run from the Save Sphere right outside of the Cavern I could never even get past the first encounter in almost 2 hours of attempts. Could be crazy bad RNG luck, but feels like there might really be something going on there. For safety's sake, I recommend saving over in the Calm Lands or the Airship if you have it already (I don't yet).
I have a First Strike weapon on Yuna made with a Return Sphere from killing Chimerageist. These can also be won from Blitzball Tournaments.
After the second battle, I remove my No Encounters gear (dropped by the Ghosts found in this dungeon, but easier to get at the Monster Arena after capturing one). This doesn't matter much, since the game disabled encounters when I began the first fight with Dark Yojimbo. However, for some reason if you run all the way back and stand on the teleporter then walk back off, it turns encounters back on, allowing you to farm additional Overdrives. Yuna's on Slayer, so I need to get her five kills. However, I also want to fish for Yojimbo's "free attack".
I don't actually know enough about the game's RNG to know if making Yojimbo do a free attack helps reduce the chance that he'll do one in his next appearance, but experimentally it seemed to work out better for me. You don't want him to use his free attack against Dark Yojimbo because it will have a 0% chance of being Zanmato, and Dark Yojimbo will have a 100% chance of killing your Yojimbo on his first turn.
After the third battle, I again attempt to draw Yojimbo's free attack. This time it goes disastrously. He absolutely refuses to do it (possibly meaning I should have just rushed to the fourth fight), and then I risk letting him attack a Tonberry, which results in his death. Then I have to resurrect him and make sure he's performed at least a couple of uses of Zanmato to restore his compatibility back to max (death is -10, Zanmato is +4, Wakizashi-all is +3).
So overall this was quite hard and I don't recommend this method for killing Dark Yojimbo. But it is possible if you're willing to throw a few hours at it, if you're absolutely determined to defeat Penance without significant Sphere Grid leveling.
That said, it's worth noting that you can use this approach to farm endgame gear and Master Spheres from Dark Yojimbo's first encounter as soon as you hit the Calm Lands, completely breaking the balance of the game. I personally rather dislike this and find it to be one detail where the Dark Aeons and Penance make FFX HD inferior to the original release. However I like most of the other International changes, like the Quick Hit rebalance, Quick Pockets, Full Break, the Expert Sphere Grid, and early Extract abilities to prevent Sphere starvation. I can't quite say the original release was better, it's just a complicated comparison.
Before I close out I want to make a note of something. There's an old formula guide for Yojimbo that has been floating around for years, dating back to the Ultimania guide. Spreadsheets and calculators have been built off of that guide, and it's wrong. One of the steps says:
F = [Compatibility/4] + [0..63]
However in reality the formula used is:
F = [Compatibility/10] + [0..63]
This can be easily confirmed, as you can use that formula to build up to a compatibility level where according to the spreadsheet or calculators, Yojimbo has a 0% chance of using Daigoro. But if you try long enough you will see him do it. Or you can build him to the point where he has a 100% chance of doing Wakizashi or better, and you'll still see Kozukas occasionally. This isn't a big deal, but I think it's important to try to counter this old piece of information as often as possible because it's so widespread, since Ultimania was such a reputable source in its heyday.
0:00 Heading to the Cavern
1:42 Dark Yojimbo 1
2:55 Dark Yojimbo 2
3:41 Enabling enemy encounters
7:10 Dark Yojimbo 3
7:38 Overdrive building
10:20 Yojimbo free attack... disaster
18:59 Dark Yojimbo 4
19:50 Overdrive building
23:30 Dark Yojimbo 5
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