Here ‘bargain’ does not refer to something bought cheaply, but to an agreement
made between two parties. When one party realizes too late that the agreement
is more to the other party’s advantages than his own, he is said to have made
a bad bargain; but as the agreement is binding on both parties, he has no
alternative to make the best of it, to accept the fact that he has lost on the
deal.

In a figurative sense, to make the best of a bad bargain is to try to be
cheerful in the face of an unhappy situation and do your best with it.

##### See also:

* Make the best of a bad job