<em>Eventually </em>means "in the course of time." So after a long period of time, the plasma reduced its temperature and atoms were created.
B: Then
In this case, the meaning of <em>then </em>is "consequently." Atoms appeared, so the first stars and galaxies formed.
C: However
<em>However </em>introduces a contrast to what has been said previously. Even though scientists know about how atoms formed, they do know how the first stars and galaxies originated.