Pakistan has been vigorously pursuing a clandestine nuclear weapons programme.

Nefarious : (typically of an action or activity) wicked or criminal.
Progressive : happening or developing gradually or in stages.
Systematic : done or acting according to a fixed plan or system; methodical.
Secretive : (of a person or an organization) inclined to conceal feelings and intentions or not to disclose information.
Clandestine : kept secret or done secretively, especially because illicit.

Synonym of Clandestine is Secretive