Everything was going smoothly until the meeting of obviously very important and powerful people in London. After that, poof! Even the 'explanation' given to Mulder in the car didn't help and we were hanging on every word. Utterly baffling.
The final scenes in Antartica also challenged my ability to suspend disbelief. Aliens etc I can handle but Mulder being shot in the head and then apparently going without sleep for 4 days I can not. And how DID Mulder get an unconcious Scully dressed (with clothes obtained from I know not where) and up a 60ft ice cute whilst being chased by aliens?