It's been a little rusty since I've seen the ending and a lot of it is debatebale so these are only my views of the events and anyone feel free to correct me if I miss anything.
Okay, the gang goes to confront Kuja and he is in Trance mode and he talks about how he wishes to destroy the Crystal which is the source of all life. He thinks that if he has to die soon (I dunno when they reveal that he has a limitied life span), that no one should be able to survive. The gang confront him and defeat him. Then Necrid comes out of the crystal He talks about hoiw he is the beginning and the end and a lot of people hate this, but I had a theory of how he was present within the story the whole time, but I can't think of it now so I'll just move on.
After defeating him the Iika tree goes crazy. Kuja is trapped inside, so Zidane goes in to rescue him. He has a tear-jerking goodbye with Dagger and Dagger-tachi make away on the Red Rose with Cid. Zidane goes into the tree and finds Kuja. He talks about how he couldn't leave his brother and the tree closes up, trapping them in there. Zidane and Kuja talk and Kuja is sorry for all that he did and some other stuff goes on that I don't remember. Then, Kuja dies. Zidane is left all alone withing the tree.
We then see a letter that the main Terran wrote to Kuja and then we flash forward to a rebuilty Alexandria. They talk about how there will be a showing of the play Be My Canary or whatever it was called, and Garnet is all sad. Then it goes through and shows each of the gang where they are now with bits of a letter that everyone debates about who is from. It is too Zidane though and thanks him and all this stuff. I personally believe it's from Vivi but anyway.
Quina is still in the marshe, eating food talking to Quale, same old, same old. Freya is talking to her love, and comments that he still doesn't remember her, but they are going to rebuild they're life. Amarant is walking towards Alexandria and meets Lani. They exchange shippy words and head off together (I think). Eiko is in an elevator with Cid and Hilda, and refers to them as Mom and Dad and they are touched and decide to adodt her. Steiner is in a room in the palace, and he and Beatrix have a sweet exchange and vow to protect Garnet together.
Then Puck (the rat boy from the beginning) is walking and spots a familiar face. He calls out, saying "Vivi", but it turns out that it is not Vivi. THe young mage replies that Vivi is his father and soon, many other black mages that look like Vivi follow him. Everyone makes their way to the area the play is held and Garnet sits on her throne where her mother was at the beginning watching.
The play begins, and the part where Marcus proclaims his love to Penelope, Marcus throws off a cloak he was wearing, revealing Zidane. Garnet is shocked, but runs down the stairs, rushing through the crowd. Her pendant falls of her and she looks back at it remembering her past and duty as a princess and now a queen. She then turns rushing to Zidane leaving it, choosing herself over her royalty, something that she was struggling with through the duration of the game. She runs over onto the stage and slaps Zidane nice and good. THey embrace and Zidane tells her he was able to stay a live in the tree for so long because everyday he sang her song. As the crowd cheers madly, we see tons of Black Mages dancing, Freya, Beatrix, Steiner, Eiko, Cid, Hilda, Amarant, Lani, and Quina among them cheering.
As the ending comes to an end, we fade to black and suddenly, Gaia and Terra smash together, and the words Final Fantasy IX appear on the screen.
We never really hear specifically about Vivi, although I like to belive he dies. The note to Zidane is very solemn sounding, and they wouldn;'t make such a big deal about Black Mages "stopping" otherwise. As for the smashing of Gaia and Terra, some say it was symbolic of many things. Garnet piecing together her past and present, royalty and herself, liek Steiner did the same with his duty and his belief and so many others did, coming full circle. Others say it really smashed. I'm not sure what I believed, although I used to have a big long theory about the whole thing, but alas, I have forgotten it now.
THis game makes me so nostalgic...It's my favorite video game of all time ^^
