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Take the website offline
Assuming you have detected that your site has been hacked, you should take it offline for the duration of the analysis and restoration process (the explanations below). This can be done in various ways and it may be necessary to perform more than one of the following tasks:
- route the domain(s) to a different server
- deactivate the web host and show a "maintenance" note
- disable the web server such as Apache (keep in mind that shutting down a web server on a system that serves virtual hosts will make all sites inaccessible)
- disconnect the server from the Internet or block access from and to the server (firewall rules)
There are many reasons why it is important to take the whole site or server offline: In the case where the hacked site is used for distributing malicious software, a visitor who gets attacked by a virus from your site, will most likely lose the trust in your site and your services. A visitor who simply finds your site offline (or in "maintenance mode") for a while will (or at least might) come back later.
Another reason is that as long as the security vulnerability exists in your website or server, the system remains vulnerable, meaning that the attacker could continue harming the system, possibly causing more damage, while you're trying to repair it. Sometimes the "attacker" is an automated script or program, not a human.
After the website or server is not accessible from outside, you should consider to make a full backup of the server, including all available log files (Apache log, FTP log, SSH log, MySQL log, system log). This will preserve data for a detailed analysis of the attack and allows you (and/or maybe others) to investigate the system separated from the "live" environment.
Today, more and more servers are virtual machines, not physical hardware. This often makes creating a full backup of a virtual server very easy because system administrators or hosting providers can simply copy the image file.