Yeah, she goes off on her own after that and you'll either engage in the Gongaga side-story with Tifa, or you'll skip it as you brought her there straight after the Golden Saucer (optional)
Gongaga side story? Refresh my memory please
Some of the Zack/Aeris angle is explained here. But Cloud isn't much help as he's not yet realised how incredibly fucked up he is right now. (he is essentially emulating Zack himself)
Gongaga is Zack's hometown and you can meet his parents in the little house to the south-east of the village.
You get the best dialogue by bringing Aeris with you here. As she was once Zack's girlfriend. I think bringing Tifa along as well gives you some additional information.
You can do this without Aeris and just Tifa after the ToA implodes, or you can do this in full with Aeris and/or Tifa if you enter Gongaga straight after the Gold Saucer (just after you receive the road vehicle from Dio)
I think it's best to do it straight away as you get to fight Reno and Rude (and steal some shit) Plus you can get Titan Materia and Deathblow here, and also see a scene between Tseng and Scarlet. You will miss all of this (minus the materia) if you decide to wait until after the ToA.
I wish the story would go somewhere. I know I need to get to the next place, but the story got all interesting with the black mages and we've seen nothing about them since.
Unfortunately there was never one time through FF9's story (as far as I got on disc 3) that really captivated me. I liked the atmosphere and everything, but never once did I actually care what was going on.
Agree 100 percent. FFIX was just not consistant enough. It had great characters and atmosphere, but was letdown by poor storyline development from Disc 3 onwards. The whole Kuja angle ruined the game, and I was disappointed to see 50% of the world map you were beginning to explore - was nothing more than deserted land.
I think if Disc 3 and 4 were handled with more care, then it would be one of the best in the series.