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I know that some viruses or trojans can install rootkits or bootkits to change system's normal behaviour; AFAIK for example filter queries for running processes or even hide active TCP ports.

My question is consider a system in which an imaginary virus/trojan installed on it that has a C&C center and this malware installed a rootkit that hides it's transmitting port. How can I detect (please suggest a program) REAL open ports on this system or detect what applications are connecting or transmitting data?

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You can't. Once your machine is infected with a rootkit / bootkit, it's no longer your computer. The malware has control of all system calls, so you have no way of identifying spoofed results. At best you can use an external device to identify what traffic is going in/out of the box.

If you're lucky, something like tcpview will trace particular TCP sockets back to a process, but you cannot possibly know whether a rootkit is spoofing such traces.

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The best way to investigate this is to mirror the port the server is on to a different port and run a packet capture on a different system using a tool like wireshark on a windows box, or tcpdump/snoop if you are doing the capture on a unix/linux box. You can then examine the packet capture to try and figure out what's going on.

Alternatively you could shut the system down, pull the hard drive, and set it up as a secondary drive on a different system from which you can run a virus scan. Make sure it's stand-alone, not on the network, and is something that you can wipe completely without losing anything important is it could get infected from the drive you are scanning.

Neither of these two methods is likely to help you though, the problem is that once a system is rooted it's essentially impossible to restore your system, even if you somehow manage to get it working you'll never be certain the infection is gone. It can also take huge amounts of time and effort to do, with failure as the likely result. The best thing you can do is to copy off your essential data and configuration files, completely wipe the system, and rebuild it from scratch as it's the only way to be sure.

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I think you mean to mirror the switch port traffic to another port, and not the server port traffic. Wireshark also works on *nix. Live CDs exist so that you do not have to 'pull the hard drive'. –  schroeder Sep 11 '12 at 14:40

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