To perceive and recognize the meaning of
To perceive directly with the intellect
He could not fathom the depth of the ocean.
She couldn't fathom the idea.
I just can't fathom out why he lied.
Another part of her couldn't fathom how a man colder than a sociopath could be working for the side of good.
We were pensive as we tried to fathom what was occurring.