OK, first the conditions that the ship is under.
The Messenger (actually named the Ark, but the players will figure that out later) has crashed landed in the mountains near Tyr. It’s bridge and central intelligence systems are offline, so it is currently in a purely reactionary state. The entire ship is life-shaped, meaning it is technically a living organism, and even (under better conditions) a semi-conscious one. Several problems plague it, however.
When it crashed, most of it’s control crew was killed. Those who were not killed have succumbed to a crippling bacterial infection. These bacteria had been taken for study from Guthay, and were in the process of being studied when the ship’s systems crashed. The organism was released into the air. When the ship’s emergency power came on and life support was restarted, the bacteria had already infected the life support system, tainting all air, water, and vital ship fluid (blood/coolant). Now the ship produces the bacteria as it cleans the air. Anyone in the ship or within half a mile of it is affected as if exposed to a mutagenic area of Rajaat’s swamp, and all fluids inside the ship (such as the water from the faucets) are treated as fluids in such a mutagenic area. However, the disease is not instantaneous, having a 6 hour incubation period, during which it can be cured. Because the disease is highly infectious, any wounds caused by slashing or piercing weapons cause infection as well, as specified in the Pristine Tower mutations in Dregoth Ascending III. In all cases, the fortitude save is DC 15, and failure by 10 or more results in the character gaining a more severe form of the disease. This form lowers their constitution by 1 and adds 1 additional mutation of a random kind for every minute after the incubation period has elapsed. If the character reaches a constitution of 0, he immediately transforms into a Guthay Fungus, which will be described later, but looks like the host when it died (ie heavily mutated), but vegetative and clinging to the ground like a plant.
The ship also has a vague sense that it is under some sort of attack. It has begun producing a number of life shaped automatons, which go about randomly attacking anything that moves. These automatons will likewise be described later.
Finally, a number of specimens taken from athas, ral, guthay, and various neighboring planetoids have been released. Most have died due to the Guthay Fungus. This means that in addition to Rhistuli corpses scattered about, there are also a number of other creatures, including many from the lifeshaping handbook, some kreen and trin, some dromites, and others. However, all species native to Guthay have survived, having already developed a resistance to the Guthay Fungus. This includes Silk Wyrms, among others.
The ship possesses a number of hazardous environmental suits, similar in design to the Green Rhul. They are known as Symbiomechs, and are equipped with their own replenishable air supply. This means that wearers are immune to the airborn affects of the Guthas Fungus. Symbiomechs are significantly less powerful than the Green Rhul, and less intelligent, but do not run the risk of going AWOL. They are suitable for only Rhistuli, Rhul-Thuans, Halflings, and very skinny Dwarves.
The medical and research bays are equipped with life-shaping equipment beyond that currently available on Athas. A skilled lifeshaper would give their arm for some of the devices found here, and a skilled Gahv-erahn could use the equipment to cure any disease known, including the one that plagues the ship. However, there are a great many Guthay Fungi near the medical and research bays, making getting there perilous at best.
The central nervous system (bridge) of the ship can be accessed. If accessed, a Life-Tender of sufficient skill could bring the systems back to order. Druids, Psions, and Wilders might find their powers particularly useful in this regard as well.
The ship reacts to any attacks on itself by releasing chemical signals throughout the ship, telling all the lifeshaped automatons to converge in the general area of the attack. This includes physical attacks, attempts to sabotage any primary systems, and defiling (see below). Also note that any spells or powers with an AOE (such as fireball) or which pass through targets do cause some damage, any may attract the ship’s ire. This is reflected by the random encounters table for that room being shifted one category higher until the ship heals itself. Conventional damage on any portion of the room heals at 5 points per round. The ship is considered to have infinite hit points for purposes of destroying it by conventional means, and has DR 10/(slashing, piercing, fire, negative energy, and electrical) on the inside. On the outside, it has DR 20, overcome by the same things.
Finally, in regards to defiling, the ship has several interesting properties. Because the ship is effectively one giant living organism, the ship registers as abundant ground for spellcasting purposes. Furthermore, defiling circles are negated slowly over time, as the ship sends blood to the decayed region and begins to repair itself. Any defiling lowers the total life level of the ship by one degree, at which it remains until the defiling circle is restored, at (3)/(((caster level)+(spell level))/2) degrees per round, at which point the whole ship is restored to full energy. Because the process involves saturating the region with contaminated “blood”, anyone within the circle from it’s barren to it’s fertile stages must take a DC 20 save each round or contract the fungus. If for any reason the entire ship is reduced to Void, the ship becomes overwhelmed by the strain and explodes, releasing a huge cloud of the Guthay Fungi to threaten the tablelands.