What if you had taken the morning after pill then had unprotected sex 30 minutes after and he ejaculated again in you?

First, the name 'plan B' should tell you that you need a plan 'A'. Go buy yourself some condoms and BC.

Secondly, the chemical in morning after pills helps to prohibit an embryo from attaching to the wall of the uterus thus avoiding pregnancy. This is not foolproof and should not be relied on as a method of birth-control. The pill's length of effectiveness depends on you metabolic rate but should last a few hours to a day.