Megan was one of the major players in the old regime – the previous president had an arcane method of infecting all the significant members of the Federation administration and senior military with a loyalty virus, and Megan was a key factor in the manufacture and administration of that program.
However, the events that led to Randol’s death also cause a knock-on effect that all the people previously involved in the distribution of the loyalty virus either died or were severely injured. In Megan’s case, she was powerful enough in her own right to avoid death, but she did spend several months recovering from debilitating injuries.
As a result of being indisposed, she missed the election and the election campaign. By the time she was able to return to society, it was all over. Nevertheless, she remains a significantly powerful individual, and Lincoln wisely decided that he could not leave her blowing in the wind. Therefore, he appointed her Presidential Assistant, a title with no basis in the Federation constitution, but nevertheless confirmed by Senate.