One type of Trojan horse likes to alter the files system.ini or win.ini. These two files are critical to Windows and control what programs are run at startup. In system.ini, there is a line called s?±shell = explorer.exe?±. A common addition to this line when the file has been altered by a Trojan horse program is ?°shell = explorer C:\<Some directory>\<Some filename>.<Some file extension>?±.:
This causes Windows to boot up the unwanted, and most likely malicious, program on startup along with other programs that would normally be booted up. The same is true for win.ini, except instead it is ?°load =?± or ?°run =?± followed by the files??s path. If you do find any suspicious lines of code, you can remove them. You can remove these by using Run to run msconfig.exe. You should also follow the path to delete the malicious file.
If this does not work, reboot your computer and hit Shift + F5 while it is loading. This will bring you into Windows Advanced Options Menu. Select the Command Prompt Option. From here, you can use ?°edit system.ini?± or ?°edit win.ini?± to remove anything that you couldn??t before.