The Messenger is encountered during The Assault on Amaranthine. It was sent by the Architect to warn the Warden-Commander of a simultaneous attack on Vigil's Keep. Should the Warden choose to stay and defend the City of Amaranthine, the Messenger can, at the discretion of the Warden-Commander, assist in the battle. After which, the Messenger can be set free or killed.
If set free, it is mentioned in the epilogue as a helpful hooded traveler with a slight lisp who aids those it comes by. Isolated incidents of the taint also occur in the areas it visits, though the traveler and said incidents are never connected.If the Commander chooses to return to Vigil's Keep (as the Disciple recommends) it presumably returns to the Architect's side and, regardless of how the Wardens deal with the Architect, follows the rest of its kind back underground.