When u have full control of the airship and the only thing left to finish the games is defeat Jecht en Yu Yevon u can get al the secret aeons and defeat those darn hard to kill Dark Aeons. All the Dark Aeons should be easy to kill with Yojimbo's 'Zanmato' except for Dark Yojimbo. When encountering Dark Yojimbo in the Cavern of the stolen Faith u'll probably kill him the first time but u have to kill him 4 times. After the first kill run up to the tunnel to encounter him the 2nd time. Now here's the problem: Yojimbo's overdrive is empty after that last battle. When u want to perform another Zanmato u'll have to give over 200000 gil to get it(sometimes he only uses wakisashi then :( )
if u succeed the 2nd battle make ur way out of the cave and u'll encounter him a third en forth time. The trick is to have alot of gil or either have auto-life or auto-phoenix on ur shield. I'm still busy trying to defeat him by collecting loads of gil in Omega Ruins. I hope this helps to get that Penance (aeon received after defeating all dark aeons)