I think the song is entitled prison sex, not to be taken as a literal meaning of having sex in prison, but just to signify that the song refers a lot to anal sex. Because the only sex you can get in prison is anal.

the song at it's whole, in my humble opinion, is about a man who was sexually abused by his father, and is now sexually abusing his son or "lamb" (lamb could signify some other important person in his life)

"It took so long to remember just what happened.
I was so young and vestal then"
-to me this is referring to when the man singing the song (maybe maynard, maybe a character he invented)about how he was suppressing a traumatic experience, but has now figured out what happened.

"you know it hurt me,
but I'm breathing so I guess I'm still alive
even if signs seem to tell me otherwise."
-this is a little more straight forward I believe. "it hurt me, but I guess I should just be thankful that I'm alive, even though I can hardly believe it myself"

"I've got my hands bound,
my head down, my eyes closed,
and my throat wide open. "
-this is how he was positioned during the abuse and also signifies how, now all grown up, he feels mentally trapped in this state.

"Do unto others what has been done to me,
Do unto others what has been done to you."
-His repressed anger from the experience is making him want to perpetuate the cycle. The only way he feels happy is by making others feel what has been done to him.

"I'm treading water,
I need to sleep a while."
-he's having a hard time accepting what has happened to him "treading water", and needs some time

"My lamb and martyr, you look so precious."
-i love this part of the song. I think this is him turning into the abuser that his father was. The person is a lamb and martyr because he's sacrificing this person for his own personal feelings. Lamb's get sacrificed, whereas martyr's sacrifice themselves. "you look so precious" is just him lusting after the person (maybe his son).

"Won't you come a bit closer,
close enough so I can smell you."
-i think this is obvious, still cool lyrics though

"I need you to feel this,
I can't stand to burn too long.
Release inside of me.
For one sweet moment I am whole. "
-in order to help him cope with what has happened to him, his only release is by actually doing the act to someone else. He needs to make them feel what he felt. When he cums into the person it's a release, and it makes him feel whole.

"Do unto you now what has been done to me,
Do unto you now what has been done. "
- I think he may just be talking about the feelings he gets while sodomizing someone are caused by the person he's raping. These feelings are similar to the feelings he experienced while being raped. So by raping someone else, he's actually raping himself emotionally. One of those pleasure from pain things.

"You're breathing so I guess you're still alive
even if signs seem to tell me otherwise."
-explained this before, except now instead of talking about him he's talking about his "lamb".

"Won't you come on a bit closer,
close enough so I can smell you."
-obvious again

"I need you to feel this.
I need this to make me whole.
Release inside of me"
-He's sunk into this state of mind now where he needs to rape in order to feel whole. He needs to get feel this release inside of him.

"For I am your witness and
blood and flesh can be trusted.(X2)
And only this one holy medium brings me peace of mind."
-Even though he's raping this person, I think, in his mind, he believes this person is martyring themselves for him. And that's why he's a witness to the martyr. Since he's a witness that implies he needs evidence of the martyrdom, and blood and flesh can be trusted. "And only this one holy medium brings me peace of mind." is obvious I think. This is the only thing that brings him happiness now. The medium is anal raping, and he loves it so much it seems holy to him.

"Got your hands bound, your head down,
your eyes closed.
You look so precious now."
-obvious, talking about the person he's raping now. It's been clear for a few lines now that the man in this song has gone completely insane. Needs to feel power over someone else by raping them in order to feel happy.

"I have found some kind of temporary sanity in this
shit, blood, and cum on my hands. "
-he's admitting he's insane, and the only way he feels normal again is by sodomizing someone.

"I've come round full circle.
My lamb and martyr, this will be over soon."
-He's become whoever did this to him. He's come full circle. He's comforting his victim by telling them it'll be over soon. (because he's crazy now and believes that the victim is a martyr and, that even though it pains the victim, the victim is willing to go through this pain for the singer to feel happy. Thus he is comforting him because he actually does feel a sick sort of caring for the person he is raping)

"You look so precious.(X6)"
-complimenting the person he is raping, cause he's insane now

This whole song tells this story about a man who sinks down and perpetuates this cycle of raping and sodomy. It's more about power than just sodomy. Sodomy is just the medium. It's about gaining complete control over someone, so complete that the person feels utterly helpless. How this utterly helpless victim grows up, and is now obsessed with doing the same thing to others. He was victimized and now, in order to gain back (in a small way) what was taken from him, he must now do this to other people.

whether the person being raped at the end of the song could be his, then, future son is up for debate. Personally I don't know. It's actually more of a minor detail in the whole song, and doesn't change the meaning of it really.

i'd like everyone to know that this is just my opinion, I don't claim to be 100% right on all this. But I really do think that this is where Maynard/Tool was trying to go with this song.