The Rookery, or Black Mesa Dragon Rookery more formally, was founded quite recently by Keenan Lane and an assortment of his associates, notably as shown, Melissa Larrabie. As his primary genetic engineer and "Leggy Blonde Conscience", she's rather taken with how awesome dragons - and the people who ride them - are.
On an alternate Earth, known as the Rookery Earth dimension, alien invaders have ravaged the planet and hundreds of others. The Combine have the upper hand on the planet, but Keenan and his cohorts hail from another version - Repurposed Earth - which saw their victory over the Combine already. Now they seek to rid dimensions of this incredibly dangerous multidimensional enemy once and for all. And with dragons by their side this will be achieved much easier!
Keenan was introduced to a number of dimensions during jaunts with his family, first to Vault Earth, and later including Paragon City where they became superheroes, Twoarth and Carramba High where they still hang out to teach, and finally the Protectorate itself. He rides Denhadarvahth, "the dark wings of the Mystery", who impressed him during a visit to the Healing Den. Of note, he personally has multiple (exact) clones at least one of which has not only his own dragon but his own family. He had used these bodies to jaunt around and return to his own, but the needs for a full-time math teacher and hero caused him to imprint his mind on the body fully.
Melissa has a companion in the Ice-Skywing Aurora, and they often roam the varied sites of Rookery, Rapture, North Aperture, and other facilities under the Rookery's control, making sure that science is being done well. She eagerly dives in to the genetic department at Carramba, and is also found on Zekira (though doesn't -yet- have a dragon there...).