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Secret Project Prerequisites Effects Notes
The Ascent to Transcendence 
The Ascent to Transcendence
Threshold of Transcendence The Voice of Planet must also have been built by any faction If you build this then you win a Transcendence Victory.
The Ascetic Virtues 
The Ascetic Virtues
Planetary Economics Increases base population limit by 2, gives +1 Police Morgan Industries in particular wants this, but any faction can appreciate the higher population limit.
The Bulk Matter Transmitter 
The Bulk Matter Transmitter
Matter Transmission Increases every base's production by 50%. Despite its in-game description, the Bulk Matter Transmitter seems to increase every base's production by 50%. By the time you can build this, ecodamage will be a serious problem. An unexpected 50% jump in your production will cause rampant fungal pops and global warming. If you anticipate its effect, however, the boost in production can be very nice, though of course it comes very late in the game.
The Citizens' Defense Force 
The Citizens' Defense Force
Intellectual Integrity Free Perimeter Defense in every base. Yang can benefit from this project: his free perimeter defenses can be destroyed by probe teams, but these cannot.
Clinical Immortality 
Clinical Immortality
Matter Editation +1 talent at every base. Doubles your votes in elections for Planetary Governor and Supreme Leader. The Peacekeepers faction already gets double votes. If you are playing as them, you'll want to get this to become Supreme Leader and win the game through a diplomacy victory. If you are playing as another faction, you need to make certain they don't get this.
The Cloning Vats 
The Cloning Vats
Biomachinery All bases are in a state of population boom.
The negative effects of the Power and Thought Control social engineering choices are eliminated.
The Cloudbase Academy 
The Cloudbase Academy
(Alien Crossfire only)
Mind/Machine Interface Free Aerospace Complex in every base. This Secret Project is extremely powerful. In general, Sky Hydroponics Labs are the best way to get food later on, and food translates to population, which translates to more energy and greater research and raw cash to rush-buy anything you need to adapt to the situation. Sky Hydroponics Labs will give 1 Nutrients for every 2 Labs normally, but for bases with Aerospace Complex, it will give 1 Nutrient for each 1 Labs, greatly boosting how much population they can support. The fact that Aerospace Complexes give constructed Needlejets and Copters extra morale levels is almost inconsequential compared to the bonus to satellites.
The Command Nexus 
The Command Nexus
Doctrine: Loyalty Free Command Center in every base.
The Cyborg Factory 
The Cyborg Factory
Mind/Machine Interface Free Bioenhancement Center in every base. It is far cheaper to build this than to build Bioenhancement Centers for each of your bases. The increase in military power that these centers provide all units made there, is quite significant.
The Dream Twister 
The Dream Twister
The Will to Power +50% to psi attack Whoever gets this will have a considerable increase in the attacking ability of their mind worms and other lifeforms.
The Empath Guild 
The Empath Guild
Centauri Empathy Builder gets commlinks for and infiltration of every faction.
Builder gets 50% more votes in Council elections
Infiltration means you can know all that your enemy does, seeing the same menus as you do for yourself. You can thus see what your enemy has in their base, what they are building, what technology they are researching, and even access their military nexus to see what military units they have. Knowing which bases you can send a stronger force to in order to take out, is of great military value.

In Alien Crossfire, the Data Angels can receive any technology that is known by at least three factions they have Infiltration. So this is an even greater use to them if they haven't already used probe teams to infiltrate everyone.

The Human Genome Project 
The Human Genome Project
Biogenetics +1 talents in every base. Prevents Prometheus Virus outbreaks.
The Hunter-Seeker Algorithm 
The Hunter-Seeker Algorithm
Pre-Sentient Algorithms Destroys incoming probe teams Alien Crossfire only: Probe teams with Algorithmic Enhancement are not destroyed, but have a lowered success rate.

There are also other ways to stop probe teams.

The Living Refinery 
The Living Refinery
Advanced Spaceflight Gives +2 Support. Even if you use clean reactors for everything you build, you may still have some older units that don't. Thus this can be useful.
The Longevity Vaccine 
The Longevity Vaccine
Bio-Engineering +50% Economy at this base for Free Market economics
-2 Drones at every base for Planned economics
-1 Drone at every base for Simple or Green economics
If you are using one base for stockpiling energy, this would be especially useful to build there.
The Manifold Harmonics 
The Manifold Harmonics
(Alien Crossfire only)
Secrets of the Manifolds Increases monolith and fungus production according to your Planet rating:
  • 0 Planet: +1 energy
  • 1 Planet: +1 nutrient, +1 energy
  • 2 Planet: +1 nutrient, +1 mineral, +1 energy
  • 3+ Planet: +1 nutrient, +1 mineral, +2 energy
The Maritime Control Center 
The Maritime Control Center
Doctrine: Initiative Free Naval Yard in every base.
+2 movement for all naval units.
Comes a bit later in the early game, and is another project that provides free facilities. It's importance is directly tied to two things: What other factions are in the game (if the Pirates are playing, then you need this!), and how important a strong Naval presence is to your game. If Naval power is relatively unimportant to you, then skip this project, but note that whoever builds it will have ships with two (2) extra movement points, making Marine strikes of coastal bases that much harder to spot!
The Merchant Exchange 
The Merchant Exchange
Industrial Base +1 energy every square at this base. You receive the +1 energy for every square you are working. If you have a large population of citizens and/or are using supply crawlers to grab energy, then this will be of greater use.
The Nano Factory 
The Nano Factory
Industrial Nanorobotics Allows units to be fully repaired when not in a base.
Halves the cost of upgrading units.
Allows your units to fully recover in the field in a single turn.
The Net-Hack Terminus 
The Net-Hack Terminus
(Alien Crossfire only)
Self-Aware Machines +1 morale to all Probe Teams.
-25% cost of Probe Team actions.
Probe teams with Fusion Reactor or higher automatically have Algorithmic Enhancement.
The Network Backbone 
The Network Backbone
Digital Sentience Eliminates penalties for Cybernetic model
+1 research for each point of Commerce at this base.
+1 research for every Network Node in the game.
The Neural Amplifier 
The Neural Amplifier
Neural Grafting +50% Psi defense. Another project that comes later on in the early game, and one of the best defensive projects in the entire game. Essentially, this gives every unit you ever build the equivalent of "Trance" ability, and can be further enhanced by actually building "Trance" units. For Marketeers, this one is highly prized, and for players pursuing a heavy Native strategy, it's equally highly prized as part of a denial strategy. Non-native based Momentum players (and some Hybrids) will generally consider this project of only secondary importance and will seldom pursue it with much vigor.
The Pholus Mutagen 
The Pholus Mutagen
Centauri Genetics +1 Ecology at every base
Your units gain combat advantages in fungus normally reserved for native life.
+1 lifecycle for any native units you breed
Unless you're one of the "Native" factions (and to a lesser extent, Morgan), this one's only marginally useful, though the ecology bonus will help you jack your mineral counts up slightly higher, but once you hit somewhere around 40, you really don't need that. Still, if you're playing Gaian, Cult, or Morgan, I'd put it fairly high on the list, and if you're playing against one of them, you'll want to pick it up just so they can't.
The Planetary Datalinks 
The Planetary Datalinks
Cyberethics You automatically learn any tech discovered by three factions you have contact with. If you have enemies that have technology superior to your own, this can be quite useful. Mostly you'll want it, just to make certain your enemies don't get it. If you commonly shared or traded tech with two allies, you'd not want an enemy to get it simply because they'd then be able to receive the technology as well.
The Planetary Energy Grid 
The Planetary Energy Grid
(Alien Crossfire only)
Adaptive Economics Free Energy Bank at every base.
+25% returns from Stockpile Energy
Even if you never plan to stockpile energy at any of your bases, the fact that it gives you a cash enhancing facility for free (no maintenance cost) at every base is an enormous boon. This project is everything that the Merchant Exchange is not, and is much more valuable because of it.
The Planetary Transit System 
The Planetary Transit System
Industrial Automation -1 Drones at all bases with population 3 and under
Any bases you found start with a population of 3
Upon completion, bases with a population of 1 or 2 immediately grow to 3.
A new base starting with 3 population, can create additional colony pods straight away. Bases can potentially replenish their small population through growth as quickly as its reduced by new colony pods being produced.

If you have enough minerals at a base, or sent by supply crawlers to it, you can potentially make colony pods faster than your population is replenished, and end up using your final population to eliminate your base to produce the final colony pod. You can then use that colony pod to start a new base with a population of three at that location.

This is arguably the most important early Secret Project. A Builder who uses ICS (lots of 1-population bases) can double to triple their population by completing this Secret Project, leading to a massive boost in energy and productivity early in the game. This Secret Project comes from Industrial Automation, the same technology that enables Supply Crawlers, thus also includes with it the ability to speed up its completion, and convert money to minerals at a better rate than usual for Secret Projects (by building the most basic Supply Crawler, then designing a supply crawler with 2 or higher armor, Trance, and other pointless early traits, then using money to upgrade from the basic Supply Crawler to the upgraded version, then cashing in the upgraded crawler for equivalent minerals).

The Self-Aware Colony 
The Self-Aware Colony
Self-Aware Machines Halves maintenance costs for facilities
If your Police rating allows use of police, counts as an extra police unit in every base.
The influx of cash you get when your maintenance costs are halved makes this project one of the fastest to pay for itself. If you're going for the economic win, this is crucial, and it's pretty important in general, because by this stage of the game, you've got a lot of maintenance every turn. A good investment, no matter how you slice it.
The Singularity Inductor 
The Singularity Inductor
Controlled Singularity Free Quantum Converter in every base. Comes too late in the game to really be useful. By this point, you've got more mineral production than you need anyway. This is an average project, at best, and too expensive for the relatively short lifespan it has.
The Space Elevator 
The Space Elevator
Super Tensile Solids Allows units with Drop Pods to perform Orbital Insertions anywhere on the planet.
Doubles production in any bases producing orbital improvements.
Removes Aerospace Complex requirements relating to orbital improvements.
If you're planning to make heavy use of Satellites to enhance your factors of production, or if you entered the space race late and want to play catch up, this project will be a huge boon! Otherwise, even as a denial project, its only average.
The Supercollider 
The Supercollider
Applied Relativity Doubles Lab output of this city. If your middle game is not energy based, then it should be. Research and technology are so vital to the middle game, and a project like this – one that doubles lab outputs at a given base – how can you not start drooling over the prospect! No matter what your faction or pre-disposition, build it before someone else does!
The Telepathic Matrix 
The Telepathic Matrix
Eudaimonia Your bases never riot.
+2 Probe Team morale.
Useful if you conquer a lot of bases as they will have increased drone activity.

Also useful since new bases won't need to build things to keep citizens from shutting down everything in drone riots.

The Theory of Everything 
The Theory of Everything
Unified Field Theory Doubles Lab output of this city. Whatever base you are using to produce research points to advance in technology, should have this built at it. Along with the various base facilities that increase lab output, plus you able to turn citizens to engineers to boost it higher, this is something that will help you greatly. Just make certain you put it a base you plan on using for labs to begin with, otherwise it'd be a massively wasteful potential.
The Universal Translator 
The Universal Translator
Homo Superior Two free technology advances upon completion.
Any number of Alien Artifacts may be cashed in at this base.
Two free technologies are a nice gift. Any alien artifacts you have can now, find later, or get from conquering an enemy that had some, can be exchanged fora free tech also. The more alien artifacts you have, the more you are going to want this.
The Virtual World 
The Virtual World
Planetary Networks All Network Nodes count as free Hologram Theatres Building network nodes is cheaper than building hologram theaters, so this will help out. Also network nodes help your labs. The University faction gets a free network node in all of its bases, so this would help them greatly. If you plan on getting this, then the turn before you do, you can take any existing hologram theaters you already have in bases with existing network nodes, and recycle them for minerals, since you won't need them anymore anyway.
The Voice of Planet 
The Voice of Planet
Threshold of Transcendence Allows construction of the Ascent to Transcendence Secret Project and the Temple of Planet facility. Any alien lifeforms you breed get a +1 Lifecycle bonus. Building this allows you to build the Ascent of Transcendence, although it may sometimes be best to wait for somebody else to build the Voice. Alien lifeforms you breed also get a +1 lifecycle bonus. If you must build the Voice yourself, start building it in your second-most productive base, then a few turns later in the most productive base, making sure it will finish in the former base first. Then when the Voice is built, switch your best base to building the Ascent!

This must also be built before you can build Temple of Planet facilities, but this is nearly inconsequential because the construction of the Voice of Planet marks the beginning of the end — if that hadn't begun already.

The Weather Paradigm 
The Weather Paradigm
Centauri Ecology Cuts terraforming times in half(except fungus removal), and gives you access to all of the advanced terraforming techniques short of Soil Enrichment. Note that even while you can build boreholes you can not tap more than 2 minerals and 2 energy maximum until certain technologies are acquired. Environmental Economics (SMAC) eliminates limits on energy. Ecological Engineering (SMAC) releases limits on minerals.
The Xenoempathy Dome 
The Xenoempathy Dome
Centauri Meditation All fungus squares are treated as roads. The rate at which your formers plant and remove fungus is doubled. All native lifeforms you breed gain a +1 lifecycle bonus. Being able to move through fungus squares allows you to get your units around faster. Native lifeform units gain at an advantage when fighting from fungus squares. Planting fungus becomes a good way to slow your enemy down and speed yourself up. Useful strategically as you can approach an enemy from fungus and spy on them or attack them unprepared.
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