To do X-files with the SFA stuff, you'd just want to start a little lower level. You can be a reasonably competent investigative type right out of the box, and well-rounded and ready to nip at the heels of grand conspiracies by about 3rd level. The investigative classes will never be combat mosters, but the idea of
investigation is well supported. I'd argue Spycraft better manages the thinking investigator than some games because by the very nature of the genre- agents need to be skilled information gatherers. The Spycraft skill feats are juicy, character-shaping abilites. You can critical and fumble with skills- a definite concern (or advantage) when you make a lot of Search checks

. The Archer Foundation section on the Fringe is all about bringing in spooky, unexplained coincidences and hints of possible supernatural or alien involvement that just barely touch upon the lives of normal folks.. As to the threat level of combat, Wound Points equal Con... There will never be a day when a high-power handgun couldn't kill you in one shot- but the critical that could do it is governed by action dice, so there's a degree of control for both players and the GM. If you want to actual do X-Files, with the PCs attached to a large investigative organization, you're even more set- the rules for using agency resources (cash, badges, databases back at the office, calling in cops) are all in place.
We do 5 level previews of all the base classes in spycraft, so I grabbed the one for Slueths so you cold see how a face-to-face investigator type (a Fox, as opposed to the more scientific, Snoop-based Mulder) progresses.
Sleuth
This is a base class.
The Archer Conspiracy’s mandate of global security rests squarely on one pillar: information. The Foundation recruits heavily from fields of expertise that can provide it with the clearest picture of what is going on in the world, from the broad scope provided by orbital satellites to the most questionable dirt from street-side snitches. It is this latter, hands-on approach to information-gathering that interests the sleuth. A sleuth provides his team with solid investigative skills and an intimate understanding of the human mind, and can be the most valuable part of any operation involving HUMINT (human intelligence).
Abilities: With his focus on basic detective work, the sleuth requires a high Wisdom to identify clues, followed by Intelligence to determine their significance. Charisma is also helpful when dealing with witnesses and the potential intervention of local authorities. Because sleuths rarely shy away from the confrontations their discoveries often provoke, they must also maintain reasonable physical abilities.
Vitality: 1d8 plus Constitution modifier per level.
Class Skills
The sleuth’s class skills and key abilities are:
Class Skill (Key Ability)
Appraise (Int)
Bureaucracy (Cha)
Concentration (Wis)
Craft (Int)
Cultures (Wis)
Demolitions (Int)
Disguise (Cha)
Driver (Dex)
Escape Artist (Dex)
Forgery (Int)
Gather information (Cha)
Hide (Dex)
Hobby (Wis)
Innuendo (Cha)
Intimidate (Str or Cha)
Knowledge (Int)
Languages (Wis)
Listen (Wis)
Open Lock (Dex)
Profession (Wis)
Search (Int)
Sense Motive (Wis)
Spot (Wis)
Surveillance (Wis)
Use Rope (Dex)
Skill Points at 1st level: (8 + Int modifier) x 4.
Skill Points at Each Additional Level: 8 + Int modifier.
Class Features
The following are class features of the sleuth.
Starting Feats: The sleuth begins play with the following feats.
Armor Proficiency (Light)
Armor Proficiency (Medium)
Weapon Group Proficiency (Melee)
Weapon Group Proficiency (Handgun)
Weapon Group Proficiency (Rifle)
Expert: The sleuth’s adds his class level (in addition to his agent level) to all education checks. Further, if the sleuth spends an action die on an education check, he rolls two dice, adding the sum of both to the total for the check. This is the sleuth’s core ability.
Interview: A huge amount of the sleuth’s work involves speaking to people. As witnesses are usually fickle, unresponsive, or simply unobservant, it takes a deft touch to both coax them into conversation and to sort out valuable comments from confused recollections and unimportant hearsay. Through a combination of instinct, psychology, and experience, the sleuth can often elicit information that would escape others. The sleuth receives a +2 to all Gather Information checks so long as there are living witnesses to question. This bonus increases by +1 at 4th level and every four levels thereafter.
Sources: The sleuth has access to an entire network of street informants, criminal snitches, journalists, industry professionals, and other sources of information. By spending 1 hour consulting his sources (either in person or by phone) he may make a favor check without spending an action die to perform an information search, adding his Charisma modifier to the result. This check takes place outside Agency channels and does not require approval from the sleuth’s Control. This ability may be used once per session.
Human Nature: The sleuth has an intimate understanding of the human mind and the telltale signs of deception. Starting at 3rd level, once per session, the sleuth may re-roll one failed Sense Motive check that targets or opposes a skill check made by any human target. He may not use this ability if he rolled an error with his first attempt. Further, he must abide by the results of the second roll, even if it is another failure.
Bonus Feat: At 4th level the sleuth gains an additional feat from either the basic skill or style feat trees. He must still meet all prerequisites for the feat before selecting it, including minimum ability scores and skill rank requirements.
Awareness: The sleuth is extraordinarily aware of the actions and behavior of others. As such he is rarely taken by surprise. At 5th level he gains a +2 competence bonus with all checks to determine awareness during surprise rounds (see the Spycraft Espionage Handbook, pg 162).
Table 3.XX: The Sleuth
Fort Ref Will Def Init Budg Gadg
Lvl BAB Save Save Save Bon Bon Pts Pts Special
1 +0 +0 +2 +2 +1 +1 2 0 Expert, interview +2, starting feats
2 +1 +0 +3 +3 +1 +1 4 1 Sources 1/session
3 +2 +1 +3 +3 +2 +2 6 1 Human nature 1/session
4 +3 +1 +4 +4 +2 +2 8 2 Bonus feat, interview +3
5 +3 +1 +4 +4 +3 +3 10 2 Alertness +2
Hope this helps,