What are the metaphors in "Sonnet 65"?

Shakespeare uses the military metaphor of a besieged city to emphasize the fragility of all that is worldly. No matter how strong the gates of such a city, even if they are made of steel, they are still subject to the decay of time. Yet Shakespeare knows of something stronger, much stronger than even the most impregnable fortress: the love immortalized in his works.
In using such a striking metaphor Shakespeare emphasizes the powerful nature of his love. This is something that will live on forever in his many poems, always able to withstand the "siege" of time. Shakespeare presents here a picture of his art which displays a considerable degree of confidence and self-assurance. He's absolutely certain that his work will attain immortality, thus achieving a great victory over the unrelenting forces of time.
https://www.poetryfoundation.org/poems/50646/sonnet-65-since-brass-nor-stone-nor-earth-nor-boundless-sea

William Shakespeare's "Sonnet 65," like many of Shakespeare's sonnets, deals with the effects of the passage of time on the person to whom the sonnet is addressed. The speaker laments that their beauty will inevitably fade but takes comfort in the fact that it can be preserved in poetry. To get this message across, Shakespeare employs several metaphors. Beauty is repeatedly compared to fragile, delicate things and contrasted with stronger, more solid objects. The argument being: if even these sturdier things cannot survive, how can beauty?
In the first quatrain:

Since brass, nor stone, nor earth, nor boundless sea,
But sad mortality o'ersways their power,
How with this rage shall beauty hold a plea,
Whose action is no stronger than a flower?

Beauty is compared to a flower—aesthetically pleasing but not strong enough to withstand the test of time when even metals and stones cannot. Mortality and the passage of time are also personified and ascribed the emotion of "rage." Personification is a type of metaphor whereby inhuman objects, concepts, or animals are imbued with human attributes.

In the next quatrain, beauty is compared to summertime, and it is summer that is personified, described as having sweet-smelling, "honey breath." This is a metaphor for summer wind, which, as a transient, insubstantial thing, cannot be expected to withstand the "wrackful siege" of time. In comparing his lover's beauty to wind, the speaker further emphasizes his point that it cannot last.

In the third quatrain, the speaker once again personifies time, here more explicitly than ever.

O fearful meditation! Where, alack,


Shall time’s best jewel from time’s chest lie hid?

Or what strong hand can hold his swift foot back?

Or who his spoil or beauty can forbid?



The speaker compares his lover's beauty to a jewel and bemoans that it is impossible to hide this jewel from time. He wonders who would be strong enough to fight time off, referring to time as a person with the pronoun "he."

The final couplet offers a bit of hope at last.
O none, unless this miracle have might,
That in black ink my love may still shine bright.

Here the speaker describes poetry as a miracle and conjures the image of his words ("black ink") shining bright with his love's beauty. Ultimately, the only things strong enough to fight time and preserve beauty are words which can capture and describe that beauty long after it has left this earth. The poem leaves us with this final metaphor of words and beauty still shining bright—that is, continuing to be visible years into the future.