It's believed that Colonel and his operator have known of Duo's existance for quite some time, especially since most of their story is told from 20 years in the past. In Netto's current timeline, Colonel's operator called Barrel passes away from old age. It's unclear if Colonel is still alive in Netto's time, since Barrel's scar-torn PET is blank and empty.

However, in Stream the possibility of time travel is introduced, which opens a great possibility of options. The Colonel that we see appear from a mysterious gate in Netto's time, usually to help Rockman or Blues out of a pinch, may be from the past, OR it could be the now solo Colonel from the current time who is without an operator. It really is hard to tell, at least until we get a translated version of the series.

Colonel is a very powerful navi, with a default sword built onto his right arm, and he's about twice the height of Rockman. He has a rightous heart, and will do absolutely anything to make sure that the Earth remains safe and peaceful.

Colonel is so COOL. >:3 Not only is he appearing in Stream, but he will be featured in the upcoming movie as well.
This character description was made for episodes that I have seen so far. It may be updated as more episodes become available.