Maybe it was once an unicellar predator that hunted bacteria which during evolution gained the "idea" of using prey cells' machinery to do some of its biochemistry.
So it didn't eat bacteria, rather plundered those.
Then during evolution it eventually lost every other piece of own biochemistry, eventually becoming a virus.
I read about the mimivirus it mentions in the article a few years ago, and it mentioned that was one hypothesis. Another is that it went the other way around; before cells were invented life was just increasingly complicated self-replicating molecules and cellular life evolved out of them. In that case the virus-like ancestors would have evolved to prey on their self-sustaining descendents.
I think the uniqueness of this virus' genes suggests that whichever direction it happened, it happened very early in the history of life.
Then during evolution it eventually lost every other piece of own biochemistry, eventually becoming a virus.