What were you doing when this message popped up? Were you using an app? Browsing the web? Charging the phone?
It's possible it might have been a popup ad or some other form of malware/adware. This is especially true if the message mentioned anything about a virus, infected, or similar. Also, if you were using Chrome and the message said "the page at <website> says."
You could try following the suggestions in this article for clearing out malware/adware if there is any.
http://www.androidcentral.com/help-my-android-has-malware
Now, if you received this message at power on or similar and the phone won't start up, then it's probably time for a new battery.
Hope this helps.