When Piya and Fokir set off at 5:30 in the morning, the going is easy. The currents are in their favor, and Piya estimates they could be back to Garjontola in a few hours. However, before long, the winds start to turn and slow them to a snail's pace. The waves grow taller as well. When the boat lurches, Piya's backpack with her equipment and data logs almost flies out. Fokir helps her tie it to the covered part of the boat. Piya wonders if she might have cell service, but doesn't know who she'd call. Finally, they reach Garjontola and see the Megha isn't there. The wind suddenly catches the roof of the boat's shelter, tearing it off entirely and taking Piya's backpack with it.
The quickness with which the storm rolls in (and in particular, the fact that things begin in Piya and Fokir's favor) reinforces how untrustworthy the natural world can be. When Piya loses her data and her instruments, it means that she'll need to reconstruct that data if she hopes to do anything with it.
Kanai notices that the water almost glows as they approach Lusibari. As they enter the huge mohona near Lusibari, Horen sends Kanai downstairs to the engine room to bail out water with Nogen. After a bit, Nogen points to the shore of Lusibari and sends Kanai back upstairs to work out how he's getting off the bhotbhoti. Horen gives Kanai a plastic bag in which to put Nirmal's notebook and then explains that he'll have to wade to shore. He asks Kanai to tell Moyna that they'll go back for Fokir as soon as the storm dies, and Kanai asks to go too.
The glowing water is a sinister image that reinforces the power of the storm to make things look strange and alien for its human inhabitants. When Kanai has to wade to shore, it represents a breakdown in how humans take control over the natural world. In this situation, he'll have to pass through the dangerous waters, rather than bypass them as he'd be able to other times.
Kanai climbs backwards down the gangplank into the hip-deep water, clutching the notebook to his chest. He turns to look back and as he does, the wind catches him and knocks him into the water. Kanai finds his feet, but the notebook is immediately carried away.
When the notebook is lost, it reinforces Nirmal's assertion that he did little with his life—even his love for theory and the stories he had to tell are carried away in the currents.