Milligan is a secret agent who was brainswept by Ledroptha Curtain, causing him to lose his memories. He later regains them, and then remembers that he is Kate Wetherall's father. He is almost always in disguise as something or other; in fact, he can change disguises in less than a minute, going from short and fat to tall and exceptionally thin. It's reasonable to believe, however, that he resembles Kate (or she resembles him), and we know for certain that he has blue eyes, is very tall, and has blonde hair that is bright yellow. However, the books don't exactly mention his true name, for Milligan himself said the name "didn't feel right". At the end of The Mysterious Benedict Society, it is revealed that the name had popped into his head because of the last promise he had made to his daughter, going to the mill again.
Milligan cares deeply about the Society, especially his biological daughter Kate. He makes every attempt possible to keep her and her friends out of danger, often to the disdain of Kate, who seems to think herself just as qualified as her father and tries to do everything he does. She succeeds most of the time, do the help of the other society members.
In the first book, Milligan had a very melancholy and depressed personality due to his brainsweeping by Curtain. This is because he had no memories - not even of his own name - and no matter what, Mr. Benedict was incapable of bringing them back. He is noticeably more cheerful despite many wounds and a broken arm when he realizes that Kate is his long-lost daughter. He is also naturally cheerful from then on, probably because his memories are coming back, though not so eternally cheerful as Kate.
Milligan also has a cautious personality to balance out his recklessness. He's been known to forbid Kate from doing anything just to keep her safe, and he's also thrown himself off of several different high places.
Milligan has an amazing affinity and talent for disguising himself using any means necessary, similar to that of his daughter. He is also a great secret agent (likely one of the government's best), much like Kate. The only weapons he ever uses is a tranquilizer dart gun, because he does not believe in causing pain. He also gardens, though whether he is any good at it or not is not mentioned.
- "You were brave to do what you did," he said slowly. "And I know you did it out of love for our friends. But if you ever do something like this again, I can promise you that Ten Men and Executives are going to be the least of your worries- do you understand?" His expression was very severe, his jaw was set, and his words were clipped and terse as if spoken with much suppressed anger. Kate burst out laughing. "Milligan," she said, "I'll bet you scare the wits out of bad guys, but as a dad you don't scare anyone very much." "She's right." Constance said. "I can tell you aren't really angry." Milligan frowned and looked at Reynie, but Reynie averted his eyes to avoid disappointing him- for he, too, had been unfazed by Milligan's stern admonition. Only Sticky, furiously polishing his spectacles in the back seat, showed the effect Milligan had hoped for. But Sticky was easily unnerved and could hardly be used as a measure. "Well," Milligan said, his face relaxing. "At least I tried."
- "... Speaking of which, the boys weren't actually touching the briefcases in the trunk, I hope?" Wondering how Milligan knew, Kate stuck her head out the office door and gave Reynie and Sticky a warning look. They nodded and tried to close the trunk as quietly as possible. "They aren't now anyway." "Good," Milligan said, picking up his duffel bag. "I'd hate to have to speak sternly to them again. It embarasses me to be so ineffective."
— Trenton Lee Stewart (The Mysterious Benedict Society and the Perilous Journey)