After the snake's defeat, the three, with the egg, are flushed down because Fassad had Salsa pull a lever to activate the drain. Wess and Kumatora appear washed up by Wess' house, but Duster and the egg both disappeared.
You later find it at the Thunder Tower in Chapter 4. A Clayman is holding it at a place nearby, but someone takes it to the Garbage Dump. You will have to fight a stronger Clayman than the original to obtain the Hummingbird Egg, called the Forlorn Junk Heap.