 Dana Scully ( Gillian Anderson ) has been deeply distraught since Fox Mulder ( David Duchovny ) was abducted by aliens . One morning , she arrives in her partner 's office to find it being searched by FBI agents . Scully subsequently learns that the Bureau 's newly promoted deputy director , Alvin Kersh ( James Pickens , Jr . ) , has launched a manhunt in search for Mulder . The investigation is being led by an FBI special agent named John Doggett . Scully and Walter Skinner ( Mitch Pileggi ) are taken to the task force 's field office to be questioned , despite protests that they would be the most qualified to lead the manhunt themselves . As Skinner is being interrogated , Scully is accosted by an unnamed person who starts asking her about Mulder . When Scully finds out that he is actually Doggett ( Robert Patrick ) , she angrily throws water in his face and leaves . 
