"Other than being effectively indestructible himself- his physical form can be re-created- and having the defensivle capabilities of an Agent, his capacity is not actually very wide. His purpose is to isolate and remove errant code from the Matrix.
"He has a limitied analysis system himself. Simple programmes he can isolate and remove entirely from the Matrix- effective destruction- more complicated programmes require a completel code analysis from a third party. The Doctor single-mindedly follows his target, gathering code information until that third party has enough information to furnish the Doctor with the isolation code.
"He is useless aainst Humans., Humans are unique; too complicated to effect, built on an entitely different principle to a computer programme, and even if you could affect one, it would just be that one, you would have to start over for the next.
"The uniqueness of the solution is an issue with more complicated programmes as well. And they cannot be isolated and removed from the Matrix so easily. They are too firmly entrenched. But... they CAN be quarantined."