Lieutenant Fraser is one of Colonel Calvin Henderson's subordinates for Operation Falcon, a UFO cleanup operation that is sent to Townsend Wisconsin after receiving a report of a "fallen angel," or, in layman's terms, a crashed UFO. The cover story Henderson hands the press and townspeople is that there is a toxic leak or somesuch nonsense, which is sufficient to get most of the people safely out of town - both away from where they can see what it is Henderson and his men are really up to, and, a secondary concern for Henderson but a concern nonetheless, safely away from the tender mercies of the UFO's occupant, a severely pissed off alien.
Unfortunately for Fraser here, the military is not yet aware that their quarry isn't the usual kind of alien they're used to dealing it. It's invisible, apparently made of pure energy, and fatal to touch because it discharges massive amounts of blinding, burning energy upon physical contact with humans. But operating under the assumption that their prey is a regular flesh and blood alien, Lieutenant Fraser is dispatched with a group of troops to "search and destroy" after the entity is spotted using an infrared scope entering a parking garage (during which we can see that despite being invisible, it's roughly humanoid in shape).
Apparently because he never saw horror movies, Fraser splits his team up into two groups upon entering the parking garage, and, although they can see one another, the two groups are about fifty to sixty feet away from one another inside the structure (it's a big garage). Interestingly, the men comprising the other team have lights mounted to their hats.
Even though the alien is crouching directly in front of Fraser and the soldier with him, neither man notices it because (duh) it's invisible. "Jackson?" asks Fraser doubtfully, and the other soldier simply replies he doesn't see anything. The Lieutenant then glances at the other two men nearby, who shake their heads dejectedly. Nothing.
Bizarrely, the creature makes no move to attack Fraser and his companion, but it does seem interested in the other two guys across the room. As with Deputy Wright earlier, it is possible this is because of their flashlights. Just as Fraser is nervously writing off what the infrared scope saw as possibly having been an animal, the alien dashes past him and charges towards the two guys with the flashlight-equipped hats.
The second it makes contact with them... fwoosh! There's an explosion of burning white light. Fraser and Jackson whirl and shield their eyes. They quickly learn the hard way that when the alien's flash goes off, proximity means nothing, as Lieutenant Fraser, despite being several feet away from the two guys the alien is actually attacking, still dies a horrible burning death as the light engulfs the entire parking garage.
Later, we see the horribly mangled, burned bodies of Fraser and his three men being wheeled into the emergency room under Colonel Henderson's supervision, and, like most X-Files baddies, Henderson doesn't look the least bit contrite. Whether Fraser and his men die or not is never stated. Scully and Dr. Oppenheim actually do treat them, but considering that nothing Oppenheim could do for Deputy Wright and the firemen earlier saved them, it's a safe bet that Fraser and the others are goners.