In the eighth season premiere "Within", his FBI partner Dana Scully (Gillian Anderson) was partnered with John Doggett (Robert Patrick), and the two worked together to find Mulder.
In the eighth season premiere "Within", John Doggett (Robert Patrick) was assigned to take Mulder's place on the X-Files. As such, he and Dana Scully (Gillian Anderson) worked together to find Mulder.