While this sonnet addresses issues of underlying mortality and existence, there is a more dominant theme that elucidates the sonnets complicated metaphors. This theme, of juxtaposing the spiritual and the physical, as well as the transitory and the permanent, supports the following interpretation. It is apparent through careful analysis of this metaphor, that the section missing which precedes "these rebel powers" (line 2), could be filled in by the words "Soiled by".
This sonnet begins with a metaphor whose meaning is further complicated by this absence of a word, or words. In the context of soil and sin, a register throughout the sonnet, there exists an acknowledgment of the idea that your body goes back to the earth after death; the body feeds the worms in the earth and henceforth feeds life. "So shalt thou feed on Death" (line 13), encourages the thought that we must constantly obsess over death; as part of human nature we must ponder our mortality, and spirituality while relating it to our ephemeral lives. In other words, we feed on death, which in turn feeds on us. So is the perpetual cycle of life. But then what worth lies in questioning that which is inevitable?
As humans we must invest in things which are temporary simply because it is our nature. The sonnet asks why we do this: "Why so large a cost, having so short a lease" (line 5). This "lease" (line 5), refers to life, which is comparatively short. This metaphor asks why humans put so much effort into life when death comes so quickly.
Should spiritual salvation be our ultimate goal? Why else would we waste time, sinning against ourselves and the higher power, not to mention the constant battle within ourselves over the importance of the temporal? The poem insists that it seems trite to spend time worrying about life on this plane. The register of this metaphor constitutes contract--the contract we keep with death to take our souls when it is time.
A main register of the poem deals with religion. In lines one and two, the soul is said to be housed in the earth, as well as in the (center of the) body. The earth is sinful because it is made of dirt and the tangible, thus the body is sinful because it is indulged in the temporal. The individual is subsequently engaged in a war within itself--between the desire for the transitory world versus the need for spirituality. This internal war between the soul and the body is hinted by the word "array"(line 2), which often connotes elements of war. This intrinsic and inevitable battle that occurs between the soul and the body, as well as the soul and God, is represented by the "rebel powers"(line 2), which force the soul to question its meaning and mortality, and hence engage in such a civil battle. The rebel compulsions are essentially the soil, the sin, of the soul.
It is because of this battle raging simultaneously between the body and the soul, the spiritual and temporal worlds, that the poor soul is soiled by the rebel powers. These are the rebel urges that instigate the war. The soul is indeed soiled by its need to question, doubt, and even obsess over the nature of sin and death, thereby forcing itself between the spiritual and the temporal elements of life.