Malicious programs and websites can do a variety of changes, including:

• Changing your homepage. This is done to redirect you to a new place, often that shows you lots of popup ads.
• Switching to make your Internet searches go somewhere else. Again, to redirect you to a new place.
• Changing your Proxy Server settings. This can make everything you do in your browser be routed through a server the bad people provide and control. They can watch it all with this one: what you fill in on forms, every page you visit, everything. (And if they stop their server your browser won't work anymore either!)
• Setting so your Internet Connection Settings are loaded off a website. Similar to changing your Proxy settings, but allowing the website to change other things too. This can make everything you do in your browser be routed through a server the bad people provide and control. They can watch it all with this one: what you fill in on forms, every page you visit, everything. (And if they stop their server your browser won't work anymore either!)
• Disabling the "Tools->Internet Options" menu and hiding the "Internet Options" control panel. This is a nasty trick that is sometimes also done when your home page is changed. Hiding/disabling the places where you can change your Internet Options makes it much harder for you to fix your home page or other browser settings that have been altered!
• Changing the animated logo on the right side of the toolbar. This is sometimes done by your Internet Provider or others when installing their software.
• Changing the window title so it has some other name instead of "Microsoft Internet Explorer". This is sometimes done by your Internet Provider or others when installing their software.
• Changing the "Prefixes" that Internet Explorer uses to add the right thing when you type a partial address. If an address you type starts with "www." these prefix settings let Internet Explorer know to add "http://". But it can be changed to somthing like "http://evil.net/" so everything is redirected through some other servers!
• Adding a special "Style Sheet" which is normally used for things like visually impaired people to set so every page shows bigger text or high contrast for easier reading. But a malicious program can use this special style sheet to change other settings in Internet Explorer every time it starts.

One or more of these changes have been made!