I think he’s referring to how we come into existence (procreation) “that’s how the world began”. and the irony that human procreation will be the cause of the end of our existence (overpopulation) “that’s how the world will end”. He’s getting busy with a girl on the grass at night, pulls out to avoid making a baby (baby cum angels fly around you), and she’s reminded that the existence of herself (and every other person) relies on being once 3(man woman child) and not just 2(man woman). They can create a world for a new human, but the act destroys the world for the rest of the humans.

especially since later in the song he says “didnt know if it was a boy or a girl”

i feel like if he explains “they become angels, fly around you” it means he has lost someone. This most likely doesnt mean their child is moving away, nor is he talking about Adam and eve separating from god. He may have felt as if his world just began finding out he had a child, and ended as they did.

This part is definitely about miscarriage. Right after he says “didn’t know then, was it a son, was it a daughter”… So the fetus was in an early stage

Isaac’s mother left his dad and took him away with her, i guess he could mean this too.

The more likely meaning is that there was to be a child between Isaac and the woman he’s talking to before she got an abortion or miscarried.

Another possibility is that Brock is making a Biblical reference to Adam and Eve being the first “two” and God being the third. This would be in line with the rest of the song which talks about humans' belief in divine power.

In the previous verse there is a very clear allusion to God which I believe is continued here. I believe when Isaac says ‘We used to be three and not two’ he refers to that in the creation story, there was man, woman and God, who was very involved in Adam and Eve’s life. Through that they had no cares and no need to search for fulfillment. But through humanity’s own mistakes, that higher being or purpose is no longer apart of our lives. We used to be three but now we are two. That’s how the world began. And this is how it will end.

Given Isaac Brock’s history of drug abuse, it’s possible these lines are referring to a calculated abortion. It was better perhaps not to raise a child in such an environment, but the regret and the doubt are still there.

The world began in life and love, but will end in death and doubt.

To add to what has been said, And that’s how the world began
And that’s how the world will end refers to the fact that this incident cannot be forgotten and things like this will happen. Just like how the world began and its probable end, it is gonna happen. He is telling his wife/ex-wife that it is not her fault.

both ideas seem very reasonable, but in support of the first one, it does seem to go with the line “everything that keeps me together is falling apart” cos if the child moves away with someone else, part of his world is being lost there (the father), and also goes with the idea that everything returns to the way it was before (the earth and the universe “exactly where you were”).

Or (more likely in my opinion), the line supports the miscarriage theory. A family expecting a child plans and prepares for it, which is why miscarriages are so emotionally devastating. Three becomes two, and in this way shatters the parents' world and puts them back where they started.

He’s referring to the birth of Earth billions of years ago (3rd had just been made) when our ancestors were simple organisms in the ocean (We were swimming in the ocean). The 3rd line is might be referring to the period before sexual reproduction when our ancestors self-reproduced, meaning there were no genders.

Isaac Brock has never been married.