"…and pondered them in her heart"

Scully is an enigma. Maybe, as a woman in a man's world, she can be nothing else but perplexing. Certainly, as a character, she is far more complex than her partner. Where Mulder is all surface, Scully is full of contradiction and depth. 

First and foremost, we know Scully as a sceptic, assigned to assist Mulder only so she could "debunk" the X Files. She is a medical doctor, with an almost encyclopedic knowledge of the vast field of medicine. In the early series, whatever phenomena Mulder encountered, Scully had a scientific term by which to explain it. And yet, she wears a gold cross on a chain, the very pendant Mrs. Scully, just before the end of 'Ascension', gives to Mulder so that he can return it to her daughter when he finds her (cf. Season Two: Episode 5 'Ascension'). It is something Mulder admits never having considered; "if she was such a sceptic, why did she wear that?" To which Mrs Scully replies, "I gave it to her on her fifteenth birthday." 

It may be that, as this is only Season Two, Scully's character hasn't yet been fully worked out, that threads are being laid to be picked up later. Certainly, in Season Three's 'Revelations', she demonstrates that the rationality of science isn't her only belief. In conversation with Mulder about the smell of a corpse, Scully refers to saints who have exhibited the same phenomena. When Mulder asks her if she believes that, she replies, "I … believe in the idea that God's hand can be witnessed. I believe He can create miracles, yes"

The arch-rationalist accepts the validity of the irrational, the voice of reason advocates the unreasonable, the seeker after scientific explanation is open to the possibility that, on occasion, there may be none.

Scully is a deeper, more rounded character than is Fox Mulder. Unlike him, she has no need to go chasing after shadows; she has heard the stories that make up our world - the ancient myths that tell us of gods and men and the more recent legends and mysteries of the scientific world - and she able to ponder all of them in her heart, recognising how each compliments the other, not having to stress over which is the empirically provable explanation of the world and our place in it.

It is this ability to live in both worlds simultaneously that enables Scully to retain her humanity in the face of all the horror she witnesses and has inflicted upon her and her family. All the way through and into Season Nine, Scully never loses her empathy for others, especially children (cf. her treatment of Gibson Praise in the two-part Season Nine opener, 'Within' & 'Without').

In this what once was the final season, Scully is said to remind Agent Doggett of Agent Mulder after she explains alien-human hybrids, bounty hunters and shape-shifters rather matter-of-factly. It may appear that we have what seems to be a role-reversal, with Scully taking on the Mulder role and Doggett taking on that of Scully. In fact, what we have is the playing out of the inevitable over-coming of Mulder by the dark forces he has been chasing all his life. Scully, having continued to grow and develop throughout the seasons, having the strength of her more fundamental grasp of reality, is left to face the ever-continuing mysteries of life while Mulder lies tortured by his demons.
There are moments when Scully comes close to succumbing - most notoriously, her cancer. Ultimately, however, she has the will and strength to rise to the heroic heights of those mythic figures of ancient times because in her neither one side nor the other - the rational or the 'spiritual' - is allowed to dominate her perception of the world. Pondering all these things in her heart, Scully achieves a balanced view of the world that saves her from Mulder's fate.