Translation:He could not fathom what had happened.
in English we often use "fathom" to mean "work out" or "understand" or "comprehend", as in "he could not work out/understand/comprehend what had happened". Confusingly a fathom is also a unit of depth equal to 6 feet, although its rarely used in day to day speech. Unless your on a boat
If you say:
"Fatter du ikke det !!!!!!"
to someone, you tell the person that he is extremely stupid. It's not an important thing to learn.
It's better to use the verb "å forstå".
In the duo-sentence the word "fatte" is used in a different setting: Han kunne ikke fatte (forstå) ..... it was impossible to understand ....
Perhaps it's not the kindest way to phrase it but it'd be good to be able to understand if it's said to you. "Fatter du ikke det?!" is a direct cognate, with all the same implication of stupidity, to English "Don't you get it?!"
(In English, however, it could be said in a gentle tone and thus be only slightly condescending.)