This article is from the Computer Viruses FAQ, by Nick FitzGerald n.fitzgerald@csc.canterbury.ac.nz with numerous contributions by others.
A COMPANION virus is one that, instead of modifying an existing file,
creates a new program which (unknown to the user) is executed instead of
the intended program. On exit, the new program executes the original
program so that things appear normal. On PCs this has usually been
accomplished by creating an infected .COM file with the same name as an
existing .EXE file. Integrity checking antivirus software that only
looks for modifications in existing files will fail to detect such
viruses.
 
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