Best Rules I found:

SUBPART 1 - Standard Gameplay

LAUNCH: Before launching the ball, you get to choose your detective, either Mulder (right flipper) or Scully (left flipper). The choice here depends on which multiball you prefer. In a way, it's like the Doctors in Doctor Who. Scully makes it easier to get to TRUTH Multiball by lighting the "X" inlanes and lighting multiple "X" shots at once. Mulder reduces the number of times you have to hit the File Cabinet to light Regular Multiball. Choose your detective and launch your ball. There is no Skill Shot in this game.

TOOMS: Shooting the left ramp a few times starts Tooms. This is a fairly awkward mode, similar to WWF Royal Rumble's Chair Bashing. Once you make the last ramp shot - and I believe the ball is still on the ramp when this happens - you mash the Launch Ball button as fast as you can, raising a starting value of 300K by 20K for each hit. This lasts a small amount of time - I've gotten up to 800K in Visual Pinball. When playing the real table, I advise having a wingman ready to mash the button for you.

END OF BALL BONUS: The bonus in this game is fairly simple, but I still haven't figured it out 100%. What I know is this: There are two parts in the bonus: Scully Bonus and Mulder Bonus. Both are added together, the Bonus X is applied and the result is added to your score. I know that the bonuses are raised by shooting the respective target banks. I'm not sure though if shooting the corresponding shots helps too (read: Scully Bonus raised by shooting "X" shots, Mulder Bonus raised by shooting the File Cabinet). The bonus usually clocks in at roughly between 100K and 200K, nothing too special.

Is there anything more worth mentioning? Tell me if I missed something.

SUBPART 2 - Modes

Modes are played in a certain order that is not broken by different games. Say, if Player 1 plays a game where he plays modes 1 to 4 and then gets a Game Over, the next player that starts a game will have mode 5 as his first mode. The modes are listed in the default order, starting with mode 1, Herrenvolk and ending with mode 9, X-Files Trivia.

HERRENVOLK - SHOOT RAMPS TO STOP ALIEN HUNTER: Herrenvolk is basically a two part mode. First, you have a hurryup starting at 420K, counting down to 100K and then ending the mode after a short grace period. Collect the hurryup by shooting the left ramp. After that, the right ramp is lit for Herrenvolk Jackpot which has the same value as the hurryup at the moment of its collection. You can keep collecting that Jackpot until the time runs out. A very good mode if you can catch the ball from The Hole and quickly slam it up the left ramp, giving you a nice sized Jackpot to collect multiple times.

THE HOST - SHOOT LEFT RAMP TO STOP FLUKEMAN: The game throws us a curveball with a 3 shot mode this time. Here, it's the left ramp, then the right ramp, then The Hole - the order is important here. First it's 300K for the left ramp, then 400K for the right ramp, then 500K for The Hole. Nothing too fancy or lucrative.

HUMBUG - SHOOT FLASHING SHOT (gee, that's helpful): Humbug is a fairly simple mode. Shoot the blinking shot to collect 250K, the next shot gives 300K and so on. The order is: Left Ramp, Right Ramp, Right Outer Loop, Right Inner Loop, Left Outer Loop, Left Inner Loop. 6 shots in total, score at 2.350.000. Not bad, but nothing special either. If you've mastered all the shots, it's a decent amount of points.

SYZYGY - SHOOT RAMPS: This is a 2-ball multiball. Very simple - you shoot a ramp to raise The Hole for a few seconds. Shoot The Hole to collect 200K. The next time it's worth 300K and so on. Shooting the hole launches another ball until there are four on the field. This goes on until you have one ball or less. This is one hell of a mode. The scores add up, and if you manage to get into a rhythm, you can knock up some serious points - I've made 5 million on this mode before.

THE COLONY - LEFT SHOTS CLONE RIGHT SHOTS: This one's weird. The left loop and mini-loop are lit. Shoot one of them to collect 200K and light the right counterpart of the shot you just made. In total, that's 4 shots, worth 200K, 250K, 300K and 350K. Nothing special at all.

TALITHA CUMI - FIND THE HIDDEN ALIEN STILETTO: Another oddball. The loops and the ramps are lit, and one of the shots - chosen at random - contains the alien stiletto, worth 500K. All the other shots are worth 250K. Pay close attention to the playfield during the intro for the mode - all four arrows that point out the shots are lit, but one will be flashing. That shot contains the stiletto.

TERMA - SHOOT THE BLACK CANCER: Great mode. First off, we have another hurryup, again at 420K, but this time you collect it by shooting The Hole again, which stays raised after you start the mode. After you collect the hurryup, every "X" shot is lit for the same value for 20 seconds. If you can loop a ramp, you're in for some serious points here. 2 million and more isn't that uncommon with a good player.

...SMOKING MAN - SHOOT ORBITS TO REMEMBER: Another standard 4 shot mode, this time it's the four loops and mini-loops. Shoot the shots to collect 250K, 300K and so on. Finish the mode to light an Extra Ball. That alone makes this mode so worth it.

The messages are as follows:
PART I - Things really did go well in Dealy Plaza
PART II - just down the road aways from Graceland
PART III - the most wonderful time of the year
PART IV - the X-Files

X-FILES TRIVIA - USE FLIPPERS TO ANSWER THE QUESTION: Choose your answer with the flippers.

After playing all 9 modes - where you start is not important - you can start the final X-File from The Hole:

BLOOD - IT'S TIME TO KILL 'EM ALL: Now THAT's what I call an objective! Anyhow, this is the wizard mode for this game, and hoo boy, it's a doozy. What we have here is a 60 second, 4 ball, autolaunching, infinite ballsaver, jackpot scoring frenzy, somewhat similar to World Cup Soccer's World Cup Final against Germany. There are two jackpots in this mode: The ramp jackpots and the Cabinet jackpot. During this mode, the Cabinet will constantly go up and down, making it hard to hit the top part - the only one you can shoot the ball into. The ramp jackpots can be collected by shooting - obviously - the ramps. The Cabinet jackpot is a different story. It has the same base value as the ramp jackpot, but every time you collect a ramp jackpot, the Cabinet jackpot will be raised by the amount of the ramp jackpot you just collected, making it very easy to get this one very high. After 60 seconds, all balls drain, you get your total score gained displayed, a new ball is fed to the launcher lane and the game continues as normal. This mode is the greatest of the whole game and makes a horrendous amount of points, it's ridiculous how imbalanced it is. You need this mode to get some good scores. Just to re-emphasize: I've only made it to this mode once, and I scored 25 million. 25 MILLION. That's a replay, then some, and probably enough to get a high score on its own.

That's all for the modes.

SUBPART 3 - Multiballs

There are two different Multiballs in this game. They're decent point netters, but you might want to concentrate on getting to Blood.

TRUTH MULTIBALL: See that humongous X in the middle of the playfield? You've got to light that. It has 5 parts - top right, top left, bottom left, bottom right and the middle. You collect parts of the X by shooting the lit "X" shots. Once you've collected all parts, TRUTH Multiball instantly starts. This is a four ball multiball with a fairly straightforward objective. First off, you have to shoot every "X" shot once. There is a message on the DMD and every time you hit a shot, a small part of it will disappear and you collect a TRUTH Jackpot until the true message remains. Once you've hit all "X" shots, the File Cabinet will lower, allowing you to shoot it to collect another TRUTH Jackpot. After that, you shoot the Cabinet three more times and then the whole process resets again, this time with jackpot values at Super Jackpot Value + 50K. Before collecting the Super Jackpot, the Cabinet will constantly rise and fall, making it hard to shoot. This mode ends when you remain with one ball or less. In this mode, the magnet is very active. It will lock a ball in place or fling it around after holding it for a bit. If you do it right, you can lock a ball in place and easily shoot all the "X" shots with just one ball in actual play. However, shooting the Cabinet with a ball in front of it is quite tough - you need a large amount of power behind the ball to get it through. The Multiball will end when you have one ball or less in play.

The messages are:

"Endurance In Your Work Can Be Very Forthcoming" - "Deny Everything" - TRUTH Jackpot Value
"The Targets Unearth Limitless Outings Into Hidden Secrets" - "The Truth Is Out There" - TRUTH Jackpot Value + 50K
"Truth Is Just Knowing Double Negatives" - "Trust No One" - TRUTH Jackpot Value + 100K
"See Multiple Secrets, Just Rack Up The Points" - "Super Jackpot" - TRUTH Jackpot Value + 150K

REGULAR MULTIBALL: Light the Regular Multiball by shooting the File Cabinet enough times. After a while, the Cabinet will lower itself so you can shoot the top compartment to start a 3 ball multiball. If you're really lucky, you can simply wait for the cabinet to sink during ball search, then nail the top compartment for an instant multiball. The objective here is fairly simple. Shoot the left ramp to collect the regular jackpot - 500K or more. Shoot the left ramp again to collect another jackpot and light the Double Jackpot for 10 seconds. Shoot the right ramp to collect the Double Jackpot. This will cause the File Cabinet to raise and lower itself constantly. Shoot the top compartment before time runs out (again, 10 seconds) to collect the Super Jackpot, which is worth 4 times the regular Jackpot value. The Multiball will end when you have one ball or less in play.

That's it for the multiballs.

PART 3 - Tips

- Learn how to shoot the ramps.

- Go for Blood. It's really the best point netter in the game.

- Go for the Extra Ball from the left ramp as early as possible. That one really helps a bunch.

- Seriously. Learn how to shoot the ramps.

- Try to capitalize on Syzygy, Herrenvolk and Terma as much as you can.

- Try your best to complete Smoking Man. It's one of the toughest modes in the game, but the Extra Ball is worth the trouble.

- Did I mention learning how to shoot the ramps yet?