Is it permissible to accept tools gifted by an employee who is responsible for them in a company, without the company's permission, and what should the recipient do with them?

This tool is owned by the company your friend works for, and he is not permitted to dispose of it except with the owner's permission. If you know that he took it without permission, then it is not permissible for you to accept it. If you have already accepted it, you must return it to its owner.