The Master of Incognito

Incognito's Master was the cheif albeit unseen antagonist of the original 13 episode anime. It's not revealed the identity of this individual however they are revealed to be a member of hellsing or at least a member of the Round Table. Integra herself states at the end that this person was deiscovered and dealt with.

Relationships(Minions)
Incognito

It's not really stated as to what kind of relationship this individual had with Incognito but given that Incognito often seemed to do as he pleased(it was never confirmed what actions were ordered and what weren't) it's possible that Incognito unlike Alucard was to his master Integra was not completely under this person's control.

Paul Wilson

Though the two never met Paul was chosen to become a vampire and served Incognito as a right hand of sorts.

Jan Valentine and Luke Valentine The Valentine Brothers

In the anime Jan and Luke ran a club that was used for recruiting and turning new vampires. Though they had no direct contact with Incognito's Master they clearly took their orders from him/her.

Trivia
It's likely that this person served as a foil(a very poor one) to Integra as Paul and Incognito did to Seras and Alucard.

This person maybe both a stand in or reference to Walter and The Major.