Way back when I was running GREAT SCREAMING HELL, there were a few glimpses of antagonistic NPCs working on things in the background. They were never able to be properly fleshed out, and this is barely more than what I had then, but it is a good jumping off point for adaptation into other games. Drop these NPCs into scenarios as actors doing their own things, intersecting for whatever reason with the scenario that the players are dealing with. If they survive, maybe they can pull on that thread.
I. The Beast
An enormous naked man, flayed head to toe. All raw steak muscle and capelike strips of scabby skin. His skull has bloomed outwards like a chrysanthemum. It hurts to look at the folded point of golden light in the center of those ivory petals. Stands in silence when there is a handler present. Only left alone when there is violence to be done.
II. Origami Android
Glossy white sufaces fold and unfold noiselessly in an ever-shifting dance of polygons. There is the impression of a face when it is in the shape of a person, a form it takes rarely outside of meetings with the Apostles. Both form and self are infinitely malleable. You see a cat down the alley, pure white; it leaps onto the embankment wall, folds into a crane, and flies away.
III. Pallid Man
Microgravity tall, corpse-pallor pale. Brittle translucent hair down to his waist. Clothing was once white, now stained and stained and stained again. A face that one cannot imagine ever expressing joy or anger, only faint and distant resigned melancholy. Smells of formaldehyde and pond scum.
Projection of a tall man in a suit sharp enough to cut. His head is a horse's skull aflame. Wears a noose like a necktie. A charmer, a flatterer, a liar. Casual, friendly condescension to everyone, like you're already old friends, like he already knows you. He does. He already knows the worst about you. It's okay. He understands.
An orangutan with silvering fur. Scars on his knuckles, a betel-leaf habit. Antique rifle; bolt action, ammo cast by hand. A yellowing book clutched in his foot. Speaks like a tenured professor who checked out a long time ago, but still feels a glimmer of hope for the future, if only these goddamn zygotes showing up in composition shut up, did some drugs, and started actually asking the right questions.
VI. The Magistrate
A fat dolphin, pointlessly re-engineered for limbs not seen since ambulocetus, as he's dependent on a walker to carry him around.. Resplendent silk robes, purple and gold. Phallic staff of office. Barely tolerated. Obscenely rich - he can afford to have fingers to put rings on. Always accompanied by some consort or another or three.
Filthy rags and matted hair. A knife dancing between fingers, never stopping. Implant ports along the temples and spine. No telling if the mind inside the cyberbrain is the original or a passenger. Cunning, rage-simmering, impatient.
A short, stocky, dark-skinned woman. A bleached stripe runs front to back through her close-shorn hair. She stands out from the crowd for a moment before she vanishes back into the anonymity. Talk to her and she's reassuringly ordinary; practical, stubborn, working-class. She'll put two bullets through a skull with a lone terse warning and no hesitation afterwards.
IX. Standard Model
A off-the-shelf android model. Cheap, bland, anonymous. Remote operated. The voice remains the same, but sometimes the vocabulary changes. Sometimes it seems to forget things it should remember. It tries to be neutral, tries to balance the others. Fails often.
X. Gold Eyes
An androgyne in officer's garb, medals pinned on their chest. No pupil, no iris, just gold like coins. Detached from all but the glory of victory by well-executed tactics, the pursuit they chase with the obsession of an artist.
An old cryopod, two generations out of date, set up on treads. The fluid within is so murky with sediment that the inhabitant cannot be made out past a blurred shadow. An ancient vocoder croaks short, near-unintelligible sentences as if the machine is in pain.
XII. The Mask
Wears a grimacing red demon mask, the kind used to scare away lesser spirits. Carries a sword, an honest antique kept sharp. Speaks slowly, cautiously, rarely. Occasionally trips over malapropisms. A hyena sleeps at their feet, sliver collar implant on its neck.
The Tree of Life
Translucent blue trunk spiralling up from pseudopod roots, splitting into thousands of fractal branches with orange-gold leaves and heavy blue-gold-pink fruit glittering in the sunsetlight. Wherever it is, it makes itself the center. Remove the sandals from your feet, for this is holy ground.
The Tree is a surviving bud of ancient alien biotech - essentially a "biosphere in a box". It can grow just about anything with sufficient raw foodstock and energy. If it really started to take off, it would grow to the size of a small continent by the time it was done. It can write the code for neogenic species in a few hours.
It's intelligent in its own way, and can be can be communicated with after a fashion, but seems to be closer to a gorilla than Solaris. It's neither hostile nor malicious. It's actually somewhat fond of humans (who knows why), going as far as to adjust its output to be more or less human appropriate, at least in terms of biochemistry. In other ways, not so much.
The Apostles want to get the Tree or one of its buds offworld, so that it can spread across human space. On paper, this is a great idea, considering how much more effective it is than traditional terraforming.
Here's the issue. Five issues, actually.
Issue one: Terraforming hypercorps are, naturally, not going to be pleased with a device that does their job faster, better, and for free.
Issue two: The Apostles are trapped planetside.
Issue three: The Tree is damaged and missing components all of which are both ancient and alien.
Issue four: The Apostles are only unified in terms of restoring and exporting the Tree. The means of both are points of contention as are end result. Rivalries brew. Other aims weave in and out.
Issue five: If the Tree were able to take root on a suitable world, it would form an environment of itself, and this environment would self-replicate. That would put any humans on that world (and its later seed worlds) as inhabitants of an ecosystem they would have little to no control over. A return - in essence if not in specifics - to the days on the savanna, at the mercy of the world.