This sonnet is very somber compared to the preceding two, with no light moments, in part because it deals seriously with a troublesome love triangle between the poet and his male and female lovers.
The first four lines characterize the poet's dilemma: he has two lovers, one who provides comfort and one the causes him to despair. The comforting angel (or lover) is a "fair man," a beautiful man or a light-haired, light-complexioned man, quite possibly the Earl of Southampton; the spirit who causes despair is a dark-skinned woman. There is some ambiguity in the phrase "colour'd ill" in that it doesn't specifically refer to a physical characteristic and may mean that she is just bad to the bone rather than merely dark-complexioned.
In the next four lines, the poet tells us that the woman--"my female devil"--is trying to influence the "better angel" to abandon the poet and become a devil, like the woman, corrupting the man's pure spirit with her evil nature. What is important here is that the two spirits have a relationship completely separate from their relationship with the poet, which is troublesome because the poet has little control over what happens between the two spirits.
The next two lines confirm the fact that what the two spirits do is out of the poet's control. He cannot tell with any certainty, although he suspects the worst, whether or not his good angel has been corrupted by the female spirit--he says, in effect, even though I might think my good angel has been corrupted, I just don't now for sure.
"But being both from me" again confirms that the relationship between the two angels is not only separate from their individual relationships with him but also that they are friends. The fact that they are friends, and have diametrically opposite effects on the poet, puts him in a very precarious position because they each have some influence over the other, but the poet seems to have little influence in the love triangle--he appears to be the victim in this triangle.
Because they are friends independent of their common relationship with the poet, when the poet says they are "in another's hell," he means to suggest that they are completely out of his control and life, again emphasizing that their relationship is independent and excludes the poet.
The couplet expresses the poet's insecurity about what interaction has occurred between the two spirits, and the phrase "my bad angel fire my good one out" has been interpreted as a reference to venereal disease--in this case, the poet is implying that their relationship became physical and resulted in the female spirit giving the male spirit a venereal disease. The word "fire" in Shakespeare's time and in this context could easily have referred to a disease. If this indeed is a reference to venereal disease, the poet is saying that he will be in doubt about their relationship until his beliefs are confirmed by the evidence of actual disease. In a less controversial context, the line simply means "until she gets rid of my good angel."
In any case, this sonnet carries a solemn tone and discusses a psychologically complex relationship among three people.