How can you bypass the security system on 1999 Bonneville it wont start and the security light is on?

While I am not aware of a way to bypass or circumvent the security system, resetting the system should fix the problem if it was somehow tripped. This can be done by diconnecting the battery (while either positive or negative side will work but I would recomment negative because of less sparks on disconnect) for a period of time (usually 10-12 seconds but I would leave it disconnected for a minute or two).