The Triumvirate of Legend, Alexandria and Eidolon formed the core leadership of the Protectorate for most of the story, with Legend being the official leader. In addition to leading several teams, they were the first responders and de facto leaders of every fight against S-Class threats across the globe.
Due to sensitive information becoming public knowledge during the Echidna attack, all of the members of the Triumvirate retired from the Protectorate. While they still participated in all Class S fights following this, they no longer took leadership positions. Legend was eventually replaced by Chevalier.
These are the cream of the crop among the Protectorate. Typically powerful heroes who lead their own departments or have some other major presence in the community. In public relations Posters that advertise these protectorate heroes posters will typically include: the Triumvirate in front, followed by Myrddin, Chevalier, Cinereal, Narwhal leader of the Guild, Rime, Exalt and Armsmaster with Dragon another member of the Guild in the back represented by a dragon suit with wings extended
Each PRT department has a corresponding Protectorate team. These teams operate out of the local Protectorate Headquarters (PHQ), maintaining regular patrols and responding to reports of villain activity.
Parahumans could request transfer to specific locations, or simply be transferred to a new location. 
The Protectorate was founded by Alexandria, Eidolon, Hero and Legend. After Hero's death, the remaining founders became the leaders of smaller teams based in different cities.
In exchange for government funding and legitimacy, the Protectorate has agreeded to follow a special set of laws laid out for capes, to accept bureaucratic oversight and cooperate with local authorities.
before there were established departments several strike teams were maintained to deal with problems that appeared around the country in the background.
Taylor on Triumvirate, a biography about the Triumvirate: "Biographies weren’t my thing, and they were especially not my thing when I was suspicious it was all made up." This was possibly the earliest piece of clever foreshadowing in the series.
Members who are cleared for, and attend endbringer fights and other S-Class threats gain a substantial pay raise. Attendance is strictly voluntary however.
↑ Parahumans IRC said: Wildbow: Armsmaster appears in the posters and such of the top Protectorate heroes. Wildbow:When they do the image of everyone standing in a 'v' formation
Parahumans IRC said: Wildbow: Nah. Legend in front, Alex and Eidolon to the left and right, respectively. Then Myrddin, Chev, Cinereal, Narwhal, Rime, Exalt, Armsmaster, Dragon suit silhouette in the background, wings echoing the wings of the PRT logo over their heads. - IRC conversation archived on Spacebattles
↑Around the time that they were a group, they were simply 'the Protectorate' or 'the guys at the top'. You could say, perhaps, that the loss of Hero splintered the team. They didn't hate each other or resent each other, but it was about time, and served as the catalyst to the group each going to their own individual cities - New York, LA, & Houston. -
Comment by Wildbow on Reddit
↑So he starts off with the Protectorate and he gets a chance to shine pretty early on. In a time when there are more heroes than there are departments, he takes on a role as a member of a strike squad. An issue arises, someone calls, and he and his team mobilize to solve the problem. - Comment by Wildbow on Armsmaster's early days
↑► Miss Mercury (Protectorate Employee) Replied on July 5th, 2011: Speaking for someone in the thick of it all, I don’t think that there’s any expectation or assumption that recent events (losing Legend, losing Myrddin, several members leaving) will change the outcome of the next attack. The Protectorate and immediately related teams only make up 25-50% of the defending side when outside of North America, and North America isn’t a likely target. There’s been no policy changes or anything of the sort in the Protectorate that point to that degree of pessmism -☿ - Excerpt from Interlude 19.y
↑ “-But they’re only picking up for the PRT. They’re running scared, hemorrhaging members. They’re falling apart, and they’re big enough in the grand scheme of things that we don’t even know the repercussions if this keeps going on. Every team that fights the Endbringers relies on the Protectorate for information, for backup, equipment and even periodic training. But even beyond that, beyond the capes, there are hundreds of millions of people around the world who are watching the Protectorate, looking to them for reassurance. Our perspectives and feelings are barely a factor in the face of those hundreds of millions of watching eyes.” - Excerpt from Imago 21.2