The vanilla guide that was released with Rubicon gave only the most basic tips for passing through a level. But the secrets and the secret levels were not covered in that guide. It was also full of errors and so vague in places it was of little use at all. This guide covers the entire scenario except for three secrets and two levels, and waypoint-to-waypoint walkthroughs for each level. The levels not included in this guide are the "vidmaster" levels. Of the secrets not revealed, two are exits to these "vidmaster" levels, and the third is just plain secret. A real vidmaster should be able to find them on his or her own.
If you look at a map, you'll notice that there are numbers scattered around the map. The red numbers are waypoints - ie the the suggested path to complete the level, while the blue numbers are secret areas.
This is your home base. You will be returning to this ship several times throughout the scenario for instructions, shield charges, and gear. Take care to pick up as much of the ammo as possible when you're here because this is where the majority of your ammo will be coming from.
Don't molest the s'pht and the s'pht'kr. They're on your side. Unless you attack them, that is.
THE NEW MONSTERS
Chamberlain: You'll only encounter one or two of these at the most. They are harmless at a distance, but if they get too close to you they'll strip your shields so fast you won't know what hit you. Another annoying aspect of the chamberlain is that it is immune to all energy-type attacks. And that includes the fusion rifle and maser.
CleanroomBob: These guys are mostly harmless. But if the major cleanroombobs (the guys in black) get hostile, they'll walk up to you and strip your shield little by little - if you let them.
Drone: The new and improved drone comes in two varieties; the normal kind that fires a blizzard of small fast bolts, and the big bad kind that fires energy cartwheels like those of the s'pht'kr - and some of these are guided. The rapid-fire bolts have more bark than bite, but don't stand still for them anyway. A sweep with the fusion rifle is usually sufficient to clear an area of drones.
Enforcer: The same old enforcer, but with a brand new toy. The new weapon has a lower firing rate, but the bolts make up for that by being guided - in addition to packing quite a wallop. If you get too close the enforcer will release an electric bolt that as often as not kills the enforcer as well as everything else around.
GI Bob aka AR Bob: These guys are more or less on your side. But be careful with that friendly fire as they are every bit as dangerous as the pfhor troopers. They drop ammo when they die.
Hulk: The hulk is no longer a moving ammo sink; they now throw grenades with the speed if not the accuracy of a baseball. The best strategy when dealing with a hulk is to keep moving and keep on pumping ammo into them. At close range, use the AR or shotguns, while the maser is probably best at long range.
Juggernaut: Don't waste your ammo on the new juggernauts. They can take about twice as much damage as the old model, and shooting at them with bullets is like trying to take out a sherman tank with a bb-gun. Fortunately, all but one of the juggernauts in this scenario can be avoided. If you must take down a juggernaut, the best weapons are the rocket launcher, the maser, and the fusion rifle. Bullets and fists are useless as the juggernaut is immune to them.
Looker: These bloated gasbags have a tendency to get underfoot and blow you up. So watch your step.
MaserBob: These Dangi employees carry one of the most lethal weapons in the entire scenario, and they don't like you. But they can't take much damage so if you jump at them with double pistols or a shotgun blast or an AR spray then you should be ok. Try not to blow them up because you want the stuff they drop.
PCM: These floating spheres come in two varieties; the kind that quietly sneak up on you and explode, and the kind that gets up your nose and then electrocutes you. The former, also known as the "smart mine", tends to appear in large numbers and is best dealt with by hosing the area with the fusion rifle. When one blows up, it tends to take the others with it. The latter is a bit harder to deal with. It is a lot faster and can take much more damage. The best weapons for dealing with it is the maser at long range and the shotguns at close range. Like the first variety, it explodes when destroyed.
Slave: These guys are completely harmless. Please leave them alone.
S'pht'Wr: The s'pht revolt on the Marathon made the pfhor realize just how dangerous they really were. As a result, they decided it was better to use a genetic hybrid s'pht rather than the real thing - at least on Pfhor Prime. The resulting s'pht'wr (meaning "twisted s'pht" or "abomination" or something) are a combination of s'pht and pfhor. They fire small fast-moving guided projectiles and are protected by an energy shield.
Thinker: The thinker caste have heads so large they can't stand - let alone walk, and instead float around in chairs protected by energy field like that of the chamberlain - meaning it's immune to energy-type attacks. They fire machine-gun bursts at close range and bouncing grenades at long range. The best way to deal with them is with the shotgun. Two or three blasts is usually sufficient.
Wasp: The wasp doesn't take too much to kill, but the venom it spits causes a fair amount of damage. They can be annoying but shouldn't be too difficult to deal with.