Stanza 2 Summary

Get out the microscope, because we’re going through this poem line-by-line.

O stay, three lives in one flea spare,
Where we almost, yea, more than married are.

As the woman raises her hand to kill the flea that is still sucking her flesh, the speaker begs her to hold off. In a desperate effort, he's like, "Wait...you can't kill the flea because...because...it represents our marriage!"
Whaaaa?
Our guess is that the speaker and the woman are not actually married. After all, she probably wouldn't be so worried about losing her honor if they were.
The flea, he says, contains three lives: his, hers, and the flea's.
Notice the ridiculously strained language in, "almost, yea, more than." He leaps from "not quite married" to transcending marriage altogether in the space of a few words. This is one slippery dude.
He even manages to turn the flea into a religious symbol, akin to the Holy Trinity, which also contains three spirits: the Father, Son, and Holy Ghost.
"Stay" doesn't mean "remain"; it means "stop" or "hold back." You can almost see the speaker leaping in front of the flea, bodyguard-style, to save ("spare") its tiny life.

This flea is you and I, and this
Our marriage bed, and marriage temple is.

The speaker's absurd argument continues on, as if he has dug himself in too deep of a hole to try climbing out now.
The flea contains the essence of both people, and their blood meets like two newlyweds in their wedding bed.
The speaker pushes the religious envelope further by describing the flea's body as a "temple" in which their marriage is consecrated.

Though parents grudge, and you, we're met,
And cloister'd in these living walls of jet.

The order of the words in these lines is confusing, but the meaning is clear enough.
We get more back-story about their relationship: her parents do not approve of their union. Or maybe they just don't want this randy guy getting all friendly with their daughter.
And it's not just the parents who have bad feelings (a "grudge") about the union. The woman herself ("you") is not thrilled, either.
To which he replies: "Too late! Haha!"
Despite the reservations of everyone, it seems, except the speaker, the symbolic marriage is already taking place in the flea's jet-black body, which functions as a church, or "cloister."
Hey, it's still probably a classier venue than Vegas. Zing!

Though use make you apt to kill me,
Let not to that self-murder added be,
And sacrilege, three sins in killing three.

She really is not too pleased with the speaker. Even he will admit that her experience and habits ("use") would naturally lead her to want to "kill" him!
But, he says, if she kills the flea she will be committing no fewer than three separate sins: murder, suicide ("self murder"), and sacrilege (or disrespecting the faith).
It's murder because his blood is in the flea. It's suicide because hers is, too. And it's sacrilege because, according to the logic of the speaker, they are married inside that-there bug.
He's got a steep mountain to climb. Normally in this situation we'd forget about the romance and settle for her giving up the death wish.
Of course, by "use" or habit, the speaker also simply means that we are accustomed to killing bugs when they bite us. Normally he'd have no problem with squashing the flea.