The storm occurs in chapter fifteen, but chapter fourteen has a few details that show readers that Timothy has been planning for the eventual storm for quite some time.
Timothy and Phillip are working on harvesting some scallops when they hear something like a rifle crack. Timothy immediately knows the danger, and he lets Phillip know that they have to make some additional preparations before the hurricane shows up. They work their way up to their hut, and Phillip realizes why Timothy chose that spot for their shelter. The highest point on the island gives them the greatest amount of protection from the hurricane's storm surge. Even with the elevation, the water comes dangerously close to drowning Phillip and Timothy. Timothy uses the remaining rope to lash their water keg high up on the tree, so it does not wash away. He also uses the rope to give themselves something to tie into once the winds, rain, and storm surge start getting really bad.
Once the storm hits, Phillip and Timothy first take shelter in their hut. The hut is eventually destroyed, and Timothy covers Phillip's body with his own. They stay flat on the ground like that for two hours. After that, the two characters are forced to move themselves to the tree where their rope lashings are. Phillip presses himself against the tree, and Timothy presses himself up against Phillip and ties the two of them to the tree. Timothy protected Phillip from much of the wind, rain, and flying debris by using his own body to shield Phillip.