Before you go to fight the final boss, there is one main thing you need to have. You need to complete the 4th Floor of Arrow, Milady, and Saizo in the Soul Matrix. This means that you need to have all three of them at Soul Level 100, which can be a daunting task if you have been selecting choices in an unbalanced way up until now, but if you're close just do some Ginko Requests to get Hangout events to bump it up a bit.

Throughout the final dungeon, you will be prompted with a total of four questions. The way you respond to these questions do not matter, and those that say they matter are wrong since I chose inconsistently with the answers provided. If you're wondering I chose two of the first options and two of the second option, but again, they do not matter.

Once you beat the final fight, which by the way I was around level 63 on Hard mode at the time of beating it, you will be given one final choice, and this one is a very important part of getting the right ending. You'll basically want to choose the second option, and you'll be on track to seeing the true ending of the game.