Aegis today retains the Cell structure it assumed when it was first created. The individual Cells are largely independent and autonomous, but able to easily share information via the HERMES computer system. By maintaining a loose connection with their parent Cell, each Cell assures that their heavy reliance on HERMES does not become a true vulnerability.

Because of the autonomy granted them by Aegis Prime, each Cell is free to interpret and carry out the ultimate goals of the organization as it sees fit. This is not to say that Aegis Prime will not step in if a Cell gets out of control. For the most part, a cell's missions are initiated by their own needs and plans. On occasion, their parent Cell or Aegis prime will mandate a mission. Cells are obligated to fulfill such mandates and may not refuse them. Rogue Cells are dealt with very harshly indeed.

Cells are free to create their own child Cells, in an attempt to be more effective. A parent Cell may receive a request for aid from the child Cell. The parent operatives are expected, but not obligated, to respond.

The primary goals currently mandated by Aegis Prime are the conclusive determination of the true goals and motivations of the various alien races currently operating on Earth. Aegis Prime ultimately hopes to determine how much threat these races pose to the continued prosperity of the human race.

Aegis' secondary objective is to learn as much as possible about the aliens' physiology, technology and psychology and to develop weapons capable of exploiting any weaknesses discovered. In the event that the alien threat can not be neutralized peacefully, Aegis wants an immediate and effective strike force capacity.

All Aegis Cells have standing orders when investigating aliens. If a clear level of threat or motivation can not be estimated, the Cell is to assume a hostile intent and neutralize, by any and all means, the alien presence.

Aegis sees the supernatural as a relatively minor menace. Indeed, it is seen as a potential weapon to be exploited in the fight against the aliens. With regards to supernatural manifestations, Aegis Prime has made it clear that emphasis should be placed on investigation and research, rather than eradication.

Aegis knows that the Black Book operates from a central underground base in the mountains near Dulce, New Mexico. The base provides storage for most of their equipment and acquired alien technology, as well as housing for a majority of their agents. Unlike Aegis Cells, the Black Book operatives are strictly controlled by the commanders at Dulce. All operation teams live in the base. Only individual spies and intelligence agents networked around the country are not. Whereas Aegis prefers to recruit influential operatives into Cells and allow them the freedom to work as they see fit, the Black Book operatives are all the equivalent of foot soldiers. The agents know very little of what the organization as a whole is doing, and for the most part blindly follow orders they receive from Dulce. This structure inhibits a flexible response to quickly evolving situations, but ensures that the integrity of the operation as a whole can not be jeopardized by the capture of any agent.

The Black Book's greatest strength lies in the pacts it has made with extraterrestrials, and the information and technology gained therein. In addition to some personal weaponry and equipment gained from the Saurians, the Black Book has a fleet of ships built with a combination of Saurian and Human technology. These hybrid craft, called TD-121s, are small interceptor-type fighter aircraft equipped with Saurian weapon and drive technology, and human control systems. The Saurian components are supplied to the Black Book complete, without the knowledge to build or repair them. Therefore maintenance of the ships requires continued Saurian cooperation. The Black Book has made some attempt to lessen this dependence. They have developed a hypersonic troop transport vessel built from technology derived from the Saurian systems in the TD-121. The transports, designated "Black Manta", are stealth aircraft capable of vertical take off and landing. Aegis managed to steal some of the Black Manta technology and combined it with Atlantean cybernetic control systems to the TD-121 only effective rival, the Aurora. Aegis has learned that the Black Book has become so entwined with the Saurians that groups of Saurian Black Book agents, referred to as The Men in Black, have been formed. These agents are believed to be altered to look human and always work in groups of three. Further, they possess superhuman strength and agility and generally carry Saurian technology.

The Book also has made several treaties with the Greys. These pacts generally involve the Black Book abducting humans and exchanging them for Grey psychic aid. The combination of Grey mind control abilities and Black Book cunning and firepower creates a lethal counterforce to Aegis operations. In at least two respects, Aegis has the upper hand over the Black Book. Aegis has managed to learn far more about Atlantean technology than the Black Book. Although Aegis is not certain why this so, Aegis seized this opportunity and exploited it as far as possible. In addition, Aegis' knowledge and abilities in the realm of psychic phenomena are far superior to that of the Black Book, despite its alliance with the Greys.