Frank Spotnitz wrote and directed this episode. On the audio commentary for the episode, Spotnitz reveals that he wanted this episode to be more about the characters than the monster. He said this was because it was Duchovny's final Monster of the Week episode and he wanted to do a tribute to Mulder and Scully. So he intentionally wrote a very basic monster so that the focus wouldn't be on it.
Spotnitz accomplished his goal well. Scully reminisces over some mementos from previous cases. She even gives her Apollo 11 medallion from Mulder to Doggett to thank him. Agent Harrison is used as a character to represent the X-Files fans. She herself is a fan of Mulder and Scully, working on all their travel expenses in accounting. Spotnitz also said that we wanted to include Danny in the episode, but couldn't because of time restraints.
As always, Mulder shows great concern for Scully. We even get to see Mulder eating sunflower seeds for one last time.
I still can't believe that Mulder would tell Doggett to fire at the sound of this voice AND that Doggett would actually fire at the sound of Mulder's voice. Luckily, Doggett hits his target half-blind.
As Spotnitz himself admits, Alone doesn't have a great story or monster. It's all about the characters, and that's why I like it. Mulder is even nice to Doggett. Alone is a fine tribute to Mulder and Scully and all the x-philes who have watched the show over the years.
The character of FBI Agent Leyla Harrison (Jolie Jenkins) was kind of interesting. Her naivete was somewhat refreshing as well as troubling, and those allusions to past adventures of Scully and Mulder were a nice trip down memory lane. It didn't seem likely to me that she would have had access to the X-Files case histories as an accountant for the FBI, but for the sake of the story we'll go with it.
That early scene when Scully shares a tender moment with Agent Doggett while packing things up for her maternity leave was very well done. That Doggett had to be even more patient with Agent Harrison was a testament to his professionalism, it showed that he really grew into his role while working those paranormal cases.
But you know what, that was a real gutsy move on the part of Mulder when he told Doggett to shoot at his voice. Perfect timing like that would be pretty dicey in a real life situation, but then again, a real life situation wouldn't present a half human/half reptile antagonist like the creature Stites turned into. Except for the tail, he sort of resembled the Gollum character in "Lord of the Rings", but creepier. Heck, Stites as a crypto-biologist was pretty creepy all by himself.
The show ended with a great, humorous exchange between Scully and Mulder on the finale of the "Fight the Future" movie involving the spaceship in Antarctica. You would have to have seen the film to know what they were talking about, as that story only got passing mention in the TV series.