The warp core is a matter and antimatter intermix chamber. It mixes the two to cause particle annihilation and thus liberate energy, which is utilized (as nighthawk notes) to power the warp drive and all other systems aboard the Starship Enterprise (and other Trek vessels).

The big question is this: If the warp core reacts matter and antimatter to get energy, where does it get the antimatter in the first place? In order to create antimatter using present technology, a very large particle accelerator such as those at CERN or Fermilab is used to create particle collisions with extremely high energies. During the annihilation of some of these matter particles, antimatter (in the form of antiprotons or positrons, perhaps both) is expelled and 'caught' using magnetic fields in vacuum.

The catch is that in order to make antimatter, you have to put enough energy into the system to account for 1/2 the amount of energy that will be liberated when your resultant antimatter reacts with matter. At least, I think this is true. Someone will, I'm sure, correct me (please!) if not. Thus, the net gain in energy that results from annihilating your antimatter comes from the released energy of the matter particles (according to e=mc^2). So, if the Enterprise warpcore is forced to expend this energy to create the antimatter in the first place, why not just use that to drive the system without all this dangerous mucking about with antimatter?

DANGER: Excessive treknology treknobabble ahead! Abort now if this will cause your head to explode!

Here's my hypothesis. Let's look at what 'facts' we do have regarding the warp core, and engage in vigorous handwaving while we assume they're all 'right' and 'consistent'.

• The warpcore reacts matter and antimatter.
• The warpcore operates by, and is designed to, 'warp' space, hence the name.
• Antimatter is, in some sense, the 'mirror image' of matter.
• The operation of the warp drive takes hellish amounts of energy.
• Starting a 'cold' warp drive is an extremely energy-intensive (and time-intensive, for safety) process.
• The U.S.S. Enterprise-D, at least, carries slush deuterium (an isotope of hydrogen useful for fusion) as 'fuel', and replenishes its supplies with Bussard collectors.

Okay. I posit that the warpcore is capable of 'bending' space in such a fashion that passing matter through the field results in the 'mirroring' of that matter; ergo, matter becomes antimatter. This flipping of matter, by the way, doesn't take nearly as much energy as 'making' antimatter. Due to the complexity of the process and the extremely dangerous nature of the resultant antimatter, this can only be done with small quantities at a time of very simple materials. Hydrogen is ideal.

So, the steps involved in making energy in the warpcore are as follows:

1. The warpcore creates a localized entry into subspace, or a field which passes matter into and out of subspace. It does this using stored power.
2. Slush deuterium is passed through this field in small quantities. It comes out the other side with a reversed charge, or as antihydrogen.
3. This antihydrogen is intermixed with unmolested slush deuterium in a precisely monitored ratio (1:1).
4. The hydrogen and antihydrogen annihilate each other, liberating energy. The amount of energy liberated is calculated by:

   e=2mc²

   ... where m=mass of each fuel, and c is the speed of light.

5. This energy is used to power the warp drive (as opposed to the warp core) to drive the ship. Some of it is diverted back into the process to keep the conversion field powered; some more of it is diverted to the operation of the ship's systems.

This process thus means that creating and reacting antimatter can suddenly be a profitable enterprise. (Sorry, couldn't resist!) You end up with the above equation's worth of energy (the total content of both the antimatter, which you 'paid' for, and the annihilated matter).

Even if the 'conversion field' took as much power as the conventional process to make antimatter, it's definitely safer, and it allows a doubling of efficiency or more though the annihilation of plain matter.

Whew. Anyone care to object/argue/correct/comment?

The warp core is rather missnamed, it does not actualy warp space, all that it does is generate high energy plasma using a controled mater/antimatter reaction. Most of the generated plasma is sent to the warp nacels which generate the actual spatial warping. The deuturium is also used to power the fusion reactors of the impulse engines and auxilury power system. The Romulans have aparently found a way to get plasma from an artificial singularity(I would guess they siphon matter from the accretion disk or the jets perdendicular to the disk)

In the following data, I have used a Galaxy-class starship as a reference. Other starship classes have similar arrangements, but they differ in details.

Physically, the warp core (formally known as Matter/Antimatter Reaction Assembly, M/ARA for short) is a long vertical tube, spanning 12 decks in total. It uses two reactants: deuterium and antideuterium. A huge deuterium tank (total volume 63,200 m³) is located on decks 27-30, and 30 antideuterium tanks, each with a volume of 100 m³, are located on deck 42. On average, a starship requires refueling approx. every three years. Starfleet maintains a dedicated fleet of tanker ships solely for the purpose of refueling ships in deep space.

Both reactant tanks connect with the warp core through reactant injectors. These devices form a steady stream on (anti)matter, and inject it to the core. The reactants come into contact on deck 36 (Main engineering), in the Reaction Chamber. This is where the Dilithium Crystals are mounted. The Dilithum Crystals are exposed to high amounts of EM radiation, which renders it porous to matter and antimatter, allowing antimatter to pass though it without reacting with it. Inside the crystals, the actual annihilation takes place, and the resulting high energy plasma is tunneled to the power transfer conduits for use in the ship's various systems (Note: Pre-TNG treknology fandom agreed that the Dilithium Crystals converted the radiation generated in the matter/antimatter reaction into electricity).

So where do the reactants come from? Space is filled with rogue hydrogen particles. However, the big dish (the deflector dish) is actually used to, as its name implies, deflect the particles. The glowing tips of the warp nacelles (called Bussard ramscoops) are used for collecting them. This is a secondary method, however, and the collected hydrogen particles are used as a reserve. Usually the ship is refueled at a starbase or via a tanker.

As for the generation of antimatter, Starfleet uses solar energy to produce it in dedicated facilities around the Federation (in Mercury, for example). Galaxy-class staships do carry a device used to generate antimatter onboard, but this requires 10 units of deuterium for each unit of antimatter produced, so it is used only when antimatter supplies are exhausted and warp flight is a necessity.