Cat urine, carpet and a very rusty floor

I would recommend popping out all the floor drain plugs, and first thoroughly scrub the floor with hot soapy water. Then put the floor plugs back in temporarily and thoroughly scrub it back down with a wire brush and CLR. Pop the floor plugs and thoroughly rinse the CLR, as its a mild acid. Reapply CLR multiple times as necessary, then thoroughly dry and apply primer. I'd recommend brush on rustoleum brown rusty metal primer.