Rootkits are both tricky and stealthy, but there are still some things that you can do if you suspect that one of your Linux system has been infected. After all, a rootkit is going to be doing something if it's to be of any value to the miscreants that deployed it. In addition, its authors will have had a hard time trying to engineer their tools to avoid everything that detection tools are going to throw at it to identify and remove it.
The bad news is that detecting rootkits takes far more insight than noticing and identifying your typical virus. Many are designed to resemble device drivers so that it's possible for them to run at a more privileged level in the operating system. Rootkits often replace a keyboard or network driver, for example. The way that modern operating systems are broken into distinct privilege "layers" and numerous modules, loaded when needed and each of which manages a distinct function within the OS, makes this possible.
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Sometimes root kits will replace commands such as netstat, du, find, ifconfig, netd, killall and lsof while they will just provide support for other malware -- allowing it to run undetected or providing access to the system through backdoors. The flexibility and modularity of operating systems is, thus, also something of a "weak link" as far as security is concerned.
When you suspect a rootkit has been installed on a system, the first thing you need to decide is what the first step ought to be. Some will say that you should immediately detach it from your network, isolating it for further analysis. Others will say that you may lose valuable insights into what the rootkit is doing if you move too quickly. Besides, depending on the role the system is playing, pulling it off the network could have drastic implications if provides a critical service. On a well designed network, your critical services will be set up in such a way that you can roll them over to another system.
If your aim is to learn as much as you can about the rootkit, rebooting the system might be a bad idea. The rootkit might be one that is confined to memory and your evidence may be gone if you reboot too soon. In any case, this – how to proceed when a rootkit is suspected -- kind of decision is one that should be made long before you have to act.
You should consider detaching from your network and, at some point, shutting down the system and booting in single user mode. The key question is what's more important -- figuring out what happened or getting the system up and working again. If you must get it online again as quickly as possible, are you prepared to make an image of the infected system for analysis? If you can, that image might provide you with important insights after the fact.