I brought up the timeline earlier. I felt it was wonky. I'm not actually sure anymore - let's lay it out.
Zidane's timeline: The group wakes up. They leave Lindblum, go through Gizamaluke's Grotto, reach Burmecia at the tail end of the Alexandrian assault. Beatrix takes them all out. They get back up, leave Burmecia, head straight for Cleyra, climb up the trunk, the storm vanishes.
Garnet's timeline: She and Steiner leave Lindblum. They head to South Gate, at which point news of Burmecia's destructions have already reached it. From there, they reach Treno, meet with Tot, take the Gargan Roo, head for Alexandria and are taken captive. Garnet meets with Queen Brahne, and Kuja puts her to sleep.
Brahne and Kuja's timeline: They leave Alexandria with an army of black mages, which goes through Gizamaluke's Grotto. They reach Burmecia and destroy the city. Zorn and Thorn are there. Zidane and his party encounter them and are defeated. Brahne, Kuja, Zorn and Thorn all go back to Alexandria. Kuja makes a stop by Treno, where he runs into Garnet, then heads back to Alexandria in time for Zorn and Thorn wait for Garnet and take her prisoner. She is taken to Brahne, Kuja puts her to sleep, and Zorn and Thorn draw the eidolons. Meanwhile, Cleyra's sandstorm shield goes down for unexplained reasons.
There's… Something that doesn't work there. Zidane goes from "there for the destruction of Burmecia, heads immediately to Cleyra, sandstorm breaks," while Dagger's entire side story happens after news of Burmecia's destruction has already spread and takes its time winding through multiple locations and then ending up a prisoner. And while all this is happening, Queen Brahne's team just move between Burmecia, Treno, Alexandria and presumably then Cleyra as the plot needs while manifesting supernatural awareness of Dagger's movement so she falls into the perfect trap.
This is probably because Queen Brahne moves around in an airship, but… We know that the airships can't move freely above the mountains; they have a limited maximum altitude that forces them to pass through the Gates. That's why the black mage army had to go through Gizamaluke's Grotto. "Doctor Tot sold Dagger out" could explain the convenient trap, but how would he have gotten word out in time?
None of this is really a problem until you start to look at it too closely and interrogate how the parts fit together, but now it bugs me. Perhaps there's an explanation, though.