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.
Top Tier Heroes
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
Regional Protectorate Teams
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. Leaders will have likely spent time with the Triumvirate before being trusted with their own teams.
Parahumans could request transfer to specific locations, or simply be transferred to a new location. 
The Wards are a subdivision of the Protectorate that underage parahumans can join. If they are still in the Wards by the time they are eighteen, Wards can be reassigned to a Protectorate team but are generally kept in one city.
The PRT administrates and reins in the Protectorate. They will withhold persecution of villains who join the Protectorate, though this was not a fact that was well known to the public.
The formation of the protectorate was initially suggested by Alexandria to Eidolon, Hero and Legend as part of a larger plan to integrate parahumans into United States society. Alexandria her self had outside backers for the plan, who influenced the development of both the plan and subsequent organization.
The appearance of Behemoth hastened the formation somewhat.
On January 18th, 1993 Alexandria, Eidolon, Hero and Legend were sworn in by the President of the United States under PRTCJ as the founding members of the United States' Protectorate. It was the first in a long series of steps that led to the formation of the PRT, the Protectorate, and in the organization of heroes worldwide. In exchange for government funding and legitimacy, the members agreed to follow a special set of laws laid out for capes, to accept bureaucratic oversight and cooperate with local authorities.
During this period the four and others operated out of a singular city, traveling to trouble spots as they appeared. This was persumably New York.
Following Hero's death, the remaining founders became the leaders of smaller teams based in different cities. Before PRT Departments were an established presence in most major american cities the Protectorate maintained several strike teams to deal with problems that appeared around the country in the background.
Started committing resources seriously to the hunt for the Slaughterhouse Nine.
Deployed in vast numbers against the Second S-class threat in Brockton Bay. A severe damage to morale happened when Cauldron's history with the Protectorate were revealed. Several heroes were killed during the action.
Had recovered from loses and had weathered the two years leading up to The Slaughterhouse Nine-Thousand being released well. They still scrambled to deal with multible strikes throughout the United states by the nine.
The Protectorate were a vanguard in the early days of the event leading the first attack on Zion. They then coordinated evacuation efforts throughout North America.
They and other groups were systematically attacked by Zion over the four days of the Morning. The instrumentality of the organization was fulfilled when they were used by Khepri to end the Gold Morning.
During the final battle in Bet New York the forces of the Protectorate and others were rallied by Chevalier.
The Organization effectively dissolved afterward with its members joining multiple successor groups.
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
↑It's not a hard and fast rule. Some teams find leadership in other ways. But before a cape really gets branded and presented to the nation at large as 'leader of [city]'s Protectorate', they'll be vetted and tested and given time with the Triumvirate. Until then, it'll often be something along the lines of... sure, you're in charge of the team until someone says different, but don't go saying you're in charge and if someone asks you if you're leading the team, deflect or be sure to say it's temporary.
↑May 1st, 1988 [...] “No. Because I’d like to propose a solution. A way to assert control. I want to band together. Form a team.”
Legend leaned against the wall. “There are teams forming already. Yes, we’d be powerful, influential, but I don’t see how that addresses the problems.”
“Simple. We do what the government’s been pushing for. We regulate. We bend to the government’s yoke, all four of us together. We follow their stipulations and regulations.”
“That sounds like a horrendously bad idea,” Eidolon spoke. “Why?”
“Because if it was us four, together? We could afford to push back if they pushed too hard, and they’d know that. And just by being there, we could make the project attractive enough to bring others in. [...] The post-baby boomer generation is growing up. Couple that with the explosion in parahuman numbers, and this situation threatens to get well out of control. We need structure and organization if we’re going to keep things intact.”
“There’s no guarantee your plan will survive contact with government,” Legend said.
“There’s one guarantee.”
“I’m estimating that it will take at least five years to establish this plan nationwide. In that span, we’ll start with only a few groups in the largest cities, we’ll gradually and gratefully accept involvement and oversight from government and law enforcement. We’ll also create a sub-group for minors with powers, so we can strictly structure their environment and development. Those are the key points. [...] I expect we’ll be able to employ the remainder of the plan, the eight-stage integration of parahumans with the public, because I will be in a position of power in the government. I, my civilian self, can be in charge of the government-sponsored superhero teams within eight years. [...] I will content myself with working to guide legislation to where we need it.” - Excerpt from Interlude 15.z
↑“You asked me for my trust, I gave it. You asked me for loyalty, I gave that to you as well. You asked me for sacrifice, and I gave that. I was content to be second place in the Protectorate, because it’s what you needed.”
The Doctor paused, then nodded slowly. “Fair enough.”
“When the shit hit the fan, when my clone divulged the ugly details to the public, I made sacrifices there too. I walked away, so the Protectorate could stand. Gave up everything.” - Excerpt from Interlude 15.z
“I, Alexandria, do solemnly affirm that I will support and defend the Constitution of the United States against all enemies, foreign and domestic; that I will bear true faith and allegiance to the same; and that I will obey the orders of the President of the United States and the orders of the director appointed over me, according to the regulations of the PRTCJ.”
Applause swelled around her. As far as the eye could see, there were crowds and flashing cameras. President Griffin extended a hand and she shook it.
↑Ridtoria: Since the original group has been disbanded/killed, if you would mind bow, how did the Triumvirate+Hero (I guess just Protectorate) function as a team in the early days? Did they stick to their singular cities and occasionally team up for big events, or did they travel around the nation with Cauldron's help to promote themselves in heroics?
↑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
↑► Space Zombie Replied on July 5th, 2011: I’m more inclined to think the PRT is making a mistake than to think they’re on the ball.
My money’s on a big-ass clusterfuck. This is the first time since Behemoth first showed that we haven’t had all our ducks in a row. May’s Leviathan attack had the lowest casualty rate we’ve ever had, but I think the next one’s going to hurt us bad. - Excerpt from Interlude 19.y
↑Protectorate is currently being run by a joint team atm. Chevalier, Alexandria and Prism are each handling different tasks. - Excerpt from Interlude 19.y