What does it mean that the prophet Muhammad is the seed of the universe, as well as its most enlightened fruit?

The truth in understanding of which you have difficulty, is so elevated and profound that the mind cannot comprehend it; it can be discerned only through the light of belief. However, we will try to make it understandable through comparisons.

When considered with regard to the wisdom in its purposes, this universe appears to have the meaning of a mighty tree. Just like a tree, this world, has branches, leaves, flowers, and fruits: the elements are like its branches, the plants its leaves, the animals its flowers, and human beings its fruits. His Name the All-Wise requires that any law of the Majestic Maker which is prevalent in trees should also be prevalent for this greatest tree. So it is a requirement of Wisdom that this tree of creation would have to be formed from a seed also; a seed which would, besides those of this world of corporeality, also have to encapsulate the models and foundations of other worlds. For the origin and essential seed of the universe, which comprises thousands of different worlds, cannot be a dried, inanimate piece of matter. Since there had been no other trees prior to that tree of creation, for sure, it is again the requirement of the Divine Name the All-Wise that the meaning or the light which constituted the seed or origin of that tree would have to be clothed in the covering of a fruit. Since a seed cannot remain naked for ever, and since at the beginning of creation it was not clothed in the coat of a fruit, and since, as was previously pointed out, among human beings the most well-known and illustrious fruit is the Prophet Muhammad, upon him be peace and blessings, who has attracted the attentions of all mankind to himself, who has caused the attentions of, in particular, half of the globe and one fifth of mankind to be fixed on himself, and through his spiritual beauties and personal virtues made the world consider him with the view of either love and amazement, then, for sure, the light which constituted the seed of the universe would be clothed in his body and appear in the form of the final fruit.

O listener! Do not deem it unlikely that this amazing, mighty universe was created out of the particular nature of a man. Why should the All-Powerful One of Majesty, Who creates a huge pine tree, resembling a world of some sort, from a seed the size of a grain, have not created or have not been able to create the universe from the light of Muhammad, upon him be peace and blessings? The tree of the universe being, like the Touba tree of Paradise, upside down, with its roots and trunk upwards and branches downwards, there is a link of light, a link in meaning, between the position of the fruit below and that of the essential seed above. The Ascension is the form of that link, that the Prophet Muhammad, upon him be peace and blessings, opened up that way; he went through saint-hood and came back with Messengership, leaving the door open to it, to some sort of ascension. The saints among his community travel in heart and spirit on that highway of light under the shadow of the Prophetic Ascension and rise to the elevated stations each according to his capacity.

Also, as argued previously, the Maker of the universe has made the universe in the form of a palace for the purposes pointed out in the answer of the first difficulty. Since the means for the accomplishment of those purposes is the Prophet Muhammad, upon him be peace and blessings, prior to the universe he would have to be under the eyes of the favor of the universe�s Maker and receive His Manifestation first of all. For the result or the fruit of something is considered first. That means the latest in existence is the first in meaning. So, since the Prophet Muhammad, upon him be peace and blessings, is both the most perfect fruit and the means for the value of all other fruits and the cause for the realization of all the purposes (for the creation of the universe), then his light would of a necessity receive the first manifestation of Divine creation.