Mother

Though the mystery of what Queen Brahne is will most likely never be solved, the truth about Brahne and Garnet's relationship is that Queen Brahne is not Garnet's biological mother. (Read more about it here)

Queen Brahne, in the beginning of the game, is shown very happy while Tantalus was performing a world famous play, "I Want To Be Your Canary". Alas, Garnet is looking very disheartened. This is because for a while now, ever since the death of the King, Garnet has sensed that Queen Brahne is different from before, but does not know what. It's an uncomfortable feeling and she is worried about it. Her mother has become a changed person and being the caring daughter that she is, Garnet sets out to uncover the truth. She only knows it's probably something not very good and thus, this is the reason why she chooses to escape from Alexandria and seek help from Regent Cid in Lindblum - also her uncle. Much to her shock, Garnet never would have expected her mother to go to such drastic measures to prevent her from leaving! She was not worried about the safety of her daughter at all -- it seemed she just wanted her body back, dead or alive. Frightened and saddened, Garnet managed to escape anyhow.

Queen Brahne is the factor that sets the story in motion -- she is why Garnet is escaping from Alexandria and she is also the reason that caused Regent Cid to become nervous and send Tantalus to kidnap Garnet and bring her to safety. The truth of the matter is that Queen Brahne, for months now, has been ordering the making of hundreds, perhaps even thousands, of Black Mage dolls in the village of Dali. They are for Queen Brahne's personal army, an army of soldiers with powerful magical attacks and if one is "killed" (figuratively speaking), she can simply order a new one to be made. It's the ultimate war solution. Garnet can hardly believe this when she discovers the dolls being made below the village of Dali -- this was not the kind mother who raised her and confused, she desperately searches for the reason why.

Garnet loves her mother very much but cannot stand nor understand her mother's uncanny greed for power. She is someone she has known all her life and has maintained a lovely relationship with; now she is cold and "evil". Garnet seeks for help to bring her mother back to her senses, a sure act of betrayal against her own mother. But her mother had changed even beyond Garnet's imagination. While Queen Brahne was under Kuja's influence, she kidnaps Garnet -- her own daughter -- and extracts all the Eidolons from her, giving orders that after, her minions may dispose of her. Queen Brahne knows that Garnet has Eidolons within her and because she is desiring power, obviously the Queen steals them all for her own personal use.

As her mother digs her own grave even deeper, Garnet becomes more and more worried. Her mother is obviously oblivious to the emotional pain she is causing her daughter. It's not until her own plan backfires that Kuja's trance is lifted off of Queen Brahne. She, herself, is shocked at what she has been dong for the past few months and is sorry she caused Garnet so much grief. As she died, Garnet feels awful that, in the end, she couldn't do anything to save her mother and what's worse was watching her mother cause the death of herself.