In Fan Fiction, a "Mary Sue" is a clichéd character that the author creates as a way of putting herself into the story. Mary Sue is often faster, smarter, stronger, and more talented than the main characters, and she flawlessly complements them in every way. The story usually revolves around her and it is her brilliant plan that saves the day. In addition, she is frequently the love interest of one or more main characters, who forsake all others to worship at her feet.
From the moment I started this story, James struck me as wrong and out of place. He is a new character to the universe, yet the other characters treat him as if he has always been there. He is stronger and faster, his actions save the day once or twice, and too much of the story centers on him. Worse yet, Gwen is madly in love with him and ready to leave Rhys to be at James' side. In fact, everyone adores James and he seems to have few flaws, if any, making him very Marty Stu-like, the male equivalent of a Mary Sue.
All of this is resolved in the end and everything is returned to normal, or whatever passes for "normal" in the Torchwood universe. However, like others, I found the story somewhat fractured and haphazard. A normal Torchwood story would focus on one or more main characters' reactions to the events around them. Unfortunately, James substituted for a main character for too much of the story, making for a very distracting and disjointed read.