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Is there any way to figure out how a rootkit made its way onto my system?
Maybe. With enough time, patience and (likely) money, anything's possible. There are a million ways for a rootkit to infect your system, such as not having anti-malware software installed and a piece of malware automatically infects your system; or you are missing a patch and someone exploits that and installs the rootkit himself. The problem with rootkits is that every potential avenue of infection could be covered up or modified so there's no way of
knowing unless you have known clean copies of log files, network captures, etc., to analyze -- and those can be very hard to come by.