This phrase describes the plane crash and the manner in which Saladin Chamcha and Gibreel Farishta, two Indians, enter England. These two men enter England by way of falling from the sky and miraculously surviving their landing in the English Channel. It is a very unorthodox way of travelling, but this is a very unorthodox novel.
Like other sentences in this part of the book describing their fall from the wrecked plane, this sentence likens their fall and entrance into England to the birth of a baby. “The aircraft cracked in half…an egg yielding its mystery” is describing the birth though not necessarily of a human baby as we are not born by hatching out of an egg. Anyway, the plane cracking in half is likened to an egg hatching and something being born. Saladin and Gibreel are being born into England. The “egg yielding its mystery” is similar to these men being born into England and a baby being born into the world. When a baby is born, the baby knows nothing about the world he/she is entering, just like their parents know nothing about them. Similarly, with these two Indian men going to England, they are arriving in a foreign land that they know nothing about, and the English most likely know nothing about them. Hence, we have our “mystery”.
The passage also suggests that their entrance into England is like fertilization as well as birth. The “seed-pod giving up its spores” is the plane-wreck introducing new genes into the English gene-pool. Here we have two Indian men arriving in London and they are described as “spores”. They are capable of spreading their foreign and “mysterious” genes throughout London like the spores of plant would spread it genes and reproduce.