Because Adama refused to network his ship's computers, the Galactica remains the only capital ship unaffected by the Cylon virus.
The peace is shattered by a coordinated nuclear strike across the Twelve Colonies. Using a backdoor in humanity's defense software, the Cylons disable the Colonial fleet's advanced systems, leaving them defenseless.
The planetary centers are decimated, and the human race is pushed to the brink of extinction.
Battlestar Galactica Miniseries Part 1 - sciphilconf.berkeley.edu
With the central government destroyed, , the Secretary of Education (and 43rd in the line of succession), is sworn in as the President of the Twelve Colonies aboard a civilian transport.