Even if lightning does not directly stike your phone line, a high voltage surge pulse can be imposed on either the power line or the phone line.
These pulses can be in excess of 200 volts.
In your case, the pulse likely came in through the phoneline.
Blew up parts on the modem, and then proceeded on to the motherboard.
Note: As an old repair tech, I would junk the entire PC. All remaining parts are suspect, and could fail at any time.
Surge protectors and UPS power supplies providesome protection, but all have a limit as to how large of a pulse they will absorb.
(They also require a solid ground connection to function at all)
None of the devices will protect you from a direct lightning hit.
When ever I go away from home,or a thunderstorm is immenent, I disconnect my modem cable from the wall. If it is a strong storm, I will unplug the PC.
For a lot of details on lightning and PCs, check out www.apc.com
Yes, their primary goal is to sell you power protection, but they have a number of good resources to help you understand the scope of the problem.
Chas