There was plenty of work to be done, and plenty of people around, though most of them had no idea what they were doing. The Moondancer had lost a third of its crew to the chaos below. While the ship was capable of functioning with a very small company, all the extra work would fall on the Spelljamming Helmsman (in this case, currently unseen below decks).
Glau was aware that their secondary helmsman had been lost, and there was only so long that Flapjack could do all the work before he would be exhausted, and the ship would be "dead in the water" (so to speak). So he set about getting others to help.
Charlie and Gunthar (and others who noticed such things) were amazed to see the sails fill with a wind that had nothing to do with the air about them. The ship picked up speed and rose further into the sky.
Now the coastline could be seen far below and the mountains to the north of Kingsport. As fast as they were going, the twisting vines were growing faster still. What had been their home was now, so quickly, mostly roots of the massive vine that grew from the ground there, and swamped with the wave that had come from the vine out to sea. It was a relief that they were high enough that they could no longer make out any details of the people, ships, or buildings below.
Then suddenly they were in a cloud and a fog hung around the ship for a moment before they burst into the bright light above. For a few minutes, the ship seemed to sail on the clouds themselves with puffy white streaming by its sides like waves on the sea.
Then Gordo called a warning from the masthead and they saw it: A nearby vine grew up through the clouds. It must have been many miles tall and a hundred feet or more across. The captain called to steer clear and the ship tacked, heading away as the vine twisted, making massive swirls in the clouds.
Further away, another vine bust through the clouds, then another. The captain had planned at first to abandon the city, but it became increasingly clear to her that they needed to abandon the world.
She looked at the closest local she could see and said with a sympathetic look, "I am so sorry. There is nothing we can do."
Then she stamped her foot on the deck and called, "Flapjack! We're leaving. Take us up and out!"