As I understand it, Lee paid for the domain name and generously donated hosting -- and had done for years. Thus, he had keys to the house, and when he decided that he owned it, nobody could stop him short of a court injunction. But apparently there was no clear legal agreement, so nothing can be done.

From the Arstechnica article:

In 2017, Christel Dahlskjaer—who was, at the time, head of Freenode staff—created a corporation, Freenode Ltd., which she immediately sold to Lee.

Sounds like some money exchanged hands.