I texted my friend and said:
Hey, are you free to talk?
He said:
Sorry, I'm working on my science project.
I said: OK, I'll leave you.
Does the highlighted sentence sound correct and natural in English?
You could use
I'll leave you alone [for now]
I'll leave you be
or
I'll leave you to it
"I'll leave you"
is not hugely wrong, but it does have hints of
"I'm packing my bags & moving out."