The peace in Alexandria is short lived. Kuja is back, and he still has the power to summon Bahamut. He unleashes the eidolon onto the town and it causes huge destruction. Garnet gathers the Knights of Pluto to issue their orders. If picked correctly, it gives both the Knights and Garnet a chance to shine in their roles. For once, the Knights won't be completely inept, and Garnet makes wise decisions as a brand new queen. (Of course, you can also totally mess it up, it doesn't really matter.)
That done, Beatrix and Steiner take to the streets of the town to battle the hordes of monsters that have appeared along with Bahamut.
Steiner: "This is it, Beatrix."
Beatrix: "I will give my all for Alexandria!"
Steiner: "Well said! Let us march on to victory!"
They both battle with gusto against the seemingly unending amounts of Mistodon monsters. They also fight well together, keeping up each others spirits and defeating wave upon wave of the monsters. Beatrix suggests that they return to the castle, as this is clearly futile, but Steiner refuses.
Steiner: "No! I cannot face the princess until we destroy all these beasts. On my honour, I vow to protect the princess, the citizens of Alexandria, and..."
"Beatrix! I... I shall protect you!"
They are interrupted by more attacks. Their relationship has taken a huge turn since the beginning of the game. While Beatrix is possibly the last person to need another's protection, the sentiment of Steiner saying that to her is huge.
Steiner: "Beatrix... there is something I must tell you!"
Beatrix: "What is it?"
Beatrix: "Save your valediction, Steiner. We'll live to see another day."
It seems like Steiner was about to express some deep feelings here, doesn't it? Clearly he's had time to think about his feelings for Beatrix, and there's nothing like almost certain death to loosen your tongue. What's more, he enters Trance as soon as the battle starts, so he's really feeling a surge of emotion. And I love Beatrix's response here. She is confident that they'll survive and has no interest in hearing words that Steiner fears will be his last - her old arrogance remains. Despite her recent melancholy, Beatrix is still a fighter and one tough general. But by now we also know that there's a lot more to her than that. Beatrix has a big heart, although it may be a little hidden underneath her aloofness and detachment from years of following orders. There's no doubt she cares deeply for Steiner.
Meanwhile, Garnet has remained in the castle, although she hears a mysterious voice and attempts to find the source. It leads her to the top of the castle, and Eiko - having also heard this Summoner's Call - joins her. By using the four jewels - the one that belonged to Alexandria and the three that Brahne took from the other kingdoms - they summon Alexander together.
While Alexander successfully defeats Bahamut, Kuja is fascinated by the power of this eidolon. Like he did with Bahamut earlier, he tries to use the Invincible to take control of Alexander for himself. However, Kuja's maker, Garland, has come to check up on him. It turns out that Kuja has gone rogue from his initial orders, and Garland uses the Invincible to destroy Alexander rather than control it. Alexander's destruction causes a huge explosion, taking out most of the castle and town along with it. Garnet and Eiko are rescued by Zidane, and they regroup in Lindblum.
Steiner also makes it to Lindblum, although he lost Beatrix in all the madness and doesn't know what happened to her. Garnet, meanwhile, due to the shock and trauma of what happened to Alexandria on top of everything else, has completely lost her voice. That girl has been through a lot.
Despite this, Garnet continues on with Zidane and the others as they attempt to track down Kuja and stop whatever he has planned. While they do find Kuja, they ultimately fail to stop him, and they all gather again in Lindblum while Cid finishes a new airship. Garnet goes missing, and Zidane begins a search for her, eventually ending up back in Alexandria.
Despite his best efforts and the help of some Tantalus friends, Zidane is unable to find Garnet. He eventually runs into Baku in the ruined courtyard of Alexandria castle, who refers to "that chick" that he saw. He takes Zidane down to the docks where they find Beatrix, who has survived the attack on Alexandria.
Her reaction to Baku is interesting, especially when compared with Steiner's.
Beatrix: "You are...Baku?"
Baku: "Yup, I'm the man who abducted yer princess!"
Beatrix: "Let us forget about that. It happened a long time ago."
Baku: "You got a big heart, unlike that knucklehead, Steiner."
While I disagree that Steiner doesn't have a big heart, he was also far more antagonistic and much less willing to forgive and forget than Beatrix is. But Beatrix is still holding onto her previous melancholy, although that's hardly surprising considering Alexandria's destruction. But perhaps she is so quick to let go of these things because she knows her own tarnished history well and is in no position to judge other people.
When Zidane tells Beatrix he's looking for Garnet, Beatrix is certain that she will be at the resting place, where Brahne is buried. She doesn't go with Zidane to find her, but she does make a request of him.
Beatrix: "If you see Princess Garnet, please tell her not to worry about Alexandria..."
"She must take care of herself first."
Alexandria is in ruins, and while it is currently undergoing reconstruction, there's nothing Garnet can do to change that. Beatrix understands that Garnet must focus on herself right now, despite the fact that I'm sure Beatrix will worry about her while she's not at Alexandria. This journey she is on will only ultimately make Garnet stronger and a more capable queen. It will also help her overcome her grief and find out more about herself. Beatrix is also probably not blind to the feelings between Zidane and Garnet. Being around him is good for her (and vice versa). Beatrix also gives Zidane a garnet to give to the princess - this will allow her to summon Bahamut.
Beatrix: "Maybe it will help the princess get through this time of uncertainty..."
Garnet does manage to let go of her guilt and grief and come out the other side of it stronger. She is surrounded by her friends, and knows Beatrix is in Alexandria taking care of things. She understands that she needs to find peace with herself before she can take the throne, and decides to continue to journey with Zidane. She knows now that she can rely on other people.