Up until now, we haven't seen Beatrix question her actions or the actions of Queen Brahne. However, in the direct aftermath of Cleyra's destruction we begin to see a new side to her on the Red Rose.
Beatrix: "My troops alone would have been more than enough to take Cleyra. Why does the queen insist on using black mages and eidolons. I didn't train all these years so I could take a backseat to anyone..."
Okay, so she's not exactly showing any remorse for the people of Burmecia and Cleyra, and is actually being quite prideful and selfish. However, in her situation it is understandable to wonder why the queen is executing such overkill methods on her targets. Beatrix has proven herself as a warrior and general time and time again, and she knows how highly capable her own troops are. She knows the eidolons and black mages aren't necessary in their efforts to secure the magical jewels the queen seeks. What's more, Beatrix worked hard to get to where she is. The idea of having to play second fiddle to someone else must infuriate her, especially when she is so proud.
As she stands on the deck of the Red Rose, Beatrix watches some black mages follow orders from one of her soldiers.
To see no difference between herself and what she sees as mindless puppets created for destruction must be a bitter pill to swallow, especially when these puppets now seem to be more useful to the queen than Beatrix and her squad. It smacks of humiliation. The black mages are soulless puppets doing whatever it is that they are commanded. They have no conscience. They have no heart. How is she any different?
While the hierarchy in Beatrix's world obviously demands that she follow the orders of the queen, the queen herself has become increasing unstable and dangerous. She clearly isn't someone who's going to listen to advisors - with the exception of Kuja at this point, I'd imagine. He is the one who sent her down this path, after all.
It is in this troubled frame of mind that Beatrix goes to see the queen, and to give her the jewel she stole from Cleyra. The queen greedily snatches it from Beatrix, and begins rambling on without a word of gratitude to Beatrix.
Brahne: "Hahaha! With this I can finally... ...No. I need one more! I must get the last jewel!"
So, for whatever Brahne has planned, she needs one more jewel. She instructs Beatrix to find it immediately. It is then, when Beatrix enquires after Garnet, that Brahne says something even more alarming.
Brahne: "We have drawn all the eidolons from her. She is no longer any use to me."
Beatrix: "What do you mean, Your Majesty?"
Brahne: "Garnet has committed a crime. I shall have her executed for stealing the jewel."
Brahne: "Don't make me repeat myself! When we get back to Alexandria, I'll have Garnet beheaded! No go! Find the last jewel!"
Brahne then begins to do some maniacal laughing. It would seem that Garnet means nothing to her anymore. Now that she's extracted the eidolons from her body, Garnet is disposable. We don't get to see more of Beatrix's reaction to what the queen has just said, as the action moves back to Zidane who have also overheard the queen's terrible plans and who use the black mage teleportation pots to get back to Alexandria before the queen to save Garnet.
Beatrix, meanwhile, must have been in shock. Despite the queens erratic behaviour and unexplained warmongering, Beatrix could never have expected to hear that she plans to execute her own daughter. It's not dissimilar to Steiner's refusal to believe his monarch was capable of terrible things. Both of them have been loyal to Brahne for a long time, and perhaps it shows just how much the queen has changed – by all accounts, she used to be a lovely person. And judging from Beatrix's later reaction, I also think that she didn't quite believe the queen would do it - that once they returned to Alexandria she would change her mind or forget she had ever mentioned doing something so terrible. Surely she would never kill her own daughter?
If Beatrix held onto these naive illusions, they are soon shattered upon her return to Alexandria.
But while she is onboard the Red Rose travelling back to Alexandria, Zidane, Freya and Vivi are already there. They run into Steiner, and together they search the castle for Garnet. They eventually find her, but she's in the clutches of Zorn and Thorn who are performing the ritual to extract the eidolons from her. The two jesters are quickly defeated and retreat, so Zidane carries the unconscious Garnet while they attempt to make their escape. They pause in the queen's chambers, as Zidane hopes that letting Garnet rest for a moment will help her. But by now, the Red Rose has reached Alexandria, and Zorn and Thorn clearly ran to the queen to inform her about what Steiner and Zidane were up to as they are only there minutes when Beatrix enters the room.
Beatrix welcomes back Steiner, although there does appear to be a bit of scorn underneath the civility. Despite their working history and the fact that Steiner is a knight of Alexandria, she has no problem battling him. There's also outwardly no sign of the uncertainty she displayed on the Red Rose. This is the final battle against Beatrix, and plays out the exact same way as the previous two - you cannot defeat her.
Beatrix: "I'll kill all enemies of Alexandria!
Never step into this land again."
You know, she sounds so arrogant, but while it's not a false statement, for me the bravado begins to ring a bit false when you know she's harbouring serious doubts. It's almost like she's trying to compensate for these heavy concerns that weigh on her.
It is actually Zidane who reminds Beatrix of her duty - perhaps he's recalling her musings on the Red Rose and is attempting to appeal to her better nature. He brings her attention to the unconscious Garnet, lying on a chair behind him.
Zidane: "As the general of Alexandria, what is your sworn duty!? Isn't it to protect Dagger - your Princess Garnet? I'm sure you know who's sitting over there."
Beatrix: "It can't be... Princess...
...So, it was true. The queen really did mean to kill her..."
Zidane's appeal is successful. Despite everything, Beatrix seems to have been living in denial of what the queen is doing - as was Steiner, who is shocked by Beatrix's words. Despite how terrible it must be to accept this truth, Beatrix can no longer ignore it and realises now how wrong she has been to follow the queen so blindly.
Beatrix: "My heart is set. All this time, I have been mistaken..."
Her heart and her will are her own again. From this point on, Beatrix becomes an ally, fully devoted to the protection of Garnet and happy to assist any way she can. Her heel-face turn may seem a little sudden, even with knowing her earlier doubts, but I blame that on the limitations of the game and the fact that she is a relatively minor character in this large game. Or perhaps it's not so abrupt if you consider that Beatrix doesn't appear to have reservations about Zidane like Steiner does. She can probably see how deeply and genuinely he cares for Garnet. Perhaps that's enough for her.
Beatrix is also not unaware of her own hand in the destruction of Burmecia and Cleyra. She immediately asks Freya for forgiveness.
Freya: "It's too late to seek forgiveness..."
...But you can still save Dagger."
Freya: "I tell you this because I acknowledge your powers. Help your princess."
It's understandable that Freya cannot forgive Beatrix, and admirable that she's being so civil about everything. Beatrix, despite some misgivings, heeds Freya's words and turns to help Garnet. Once again, she's using her impressive powers, but this time she is using it to heal rather than kill. It takes some time - all the while Zorn and Thorn are there, exclaiming that the spell they cast can not be undone - but Beatrix's white magic prevails, and Garnet awakens just as Queen Brahne arrives.
Again, the only thing the queen cares about is Garnet's eidolons. Once she confirms they've been extracted from her, she instructs Zorn and Thorn to throw her in the prison. But Beatrix defies the queen directly.
Beatrix: "Your Majesty, it is my duty to protect the princess. I beg you, reconsider. Please do not harm the princess anymore."
While she's asking the queen to change her mind, in her next breath Beatrix then tells Zidane and the others to leave. She knows her words will have no effect. They move to leave, although Freya stays to stand by Beatrix's side. It's something that is a testament to Freya's character. Despite the fact that Beatrix had no small hand in the destruction of Burmecia and Cleyra, she recognises that right now, the best thing she can do is fight beside her former enemy. The queen cares not that her trusted general has betrayed her, and simply tells Zorn and Thorn to get rid of them before she leaves, completely ignoring Garnet.
Beatrix and Freya take on the monster that Zorn and Thorn set on them, giving time for Zidane and the others to make their getaway. This is the first time Beatrix is a playable character, and you get to have fun with her abilities for the first time! It's nice not to have them directed at your party anymore.
While Beatrix and Freya are fighting, Steiner decides to stay in Alexandria and help them, fearing what the queen will do to them. He asks Zidane to take care of the Princess and get her to Treno, before he runs back into the queens room, while Zidane, Garnet and Vivi make their escape.
Steiner: "The queen will never forgive them. She will kill them both..."
Steiner rejoins Beatrix and Freya, and joins their fight against seemingly endless monsters set on them by Zorn and Thorn. It's looking a bit bleak for them, and it'll be a while before we return to Alexandria...