Sounds like you haven't read about nagios at all. Normally, there are no agents. If there are, they could be any number of methods, such as ntclients, external nagios installations using nsca, etc.
From your description, it sounds like you might simply be having a problem with pinging the device at one point, and after that, the other services get all backed up, due to some excessive timeouts, or something.
Since you are new to nagios, you have no choice but to start from the beginning. i.e. the docs.