Atanwe is one of Morgan Everett's only means of physically communicating with the outside world, as Everett is bound to his home at all times, due to Majestic 12's control over Paris. He is a close associate, responsible for conveying any persons of interest to Everett's place of residence, procuring research material, and if need be, executing traitors and other targets that threaten his superior.
If Jock is killed in Area 51 by the bomb the fake mechanic put in his helicopter, then Everett consoles JC by telling him that he has ordered Atanwe to kill the mechanic. In what is likely an oversight, this occurs even if JC killed Atanwe in Everett's residence when the latter is no longer invincible.