When it comes to shutting down the most powerful atom smasher ever built, it's not simply a question of pressing the off switch.

In the French-Swiss countryside on the far side of Geneva, staff at the Cern particle physics laboratory are taking steps to wind down the Large Hadron Collider. After the latest run of experiments ends next month, the huge superconducting magnets that line the LHC's 27km-long tunnel must be warmed up, slowly and gently, from -271 Celsius to room temperature. Only then can engineers descend into the tunnel to begin their work.

The machine that last year helped scientists snare the elusive Higgs boson – or a convincing subatomic impostor – faces a two-year shutdown while engineers perform repairs that are needed for the collider to ramp up to its maximum energy in 2015 and beyond. The work will beef up electrical connections in the machine that were identified as weak spots after an incident four years ago that knocked the collider out for more than a year.

The accident happened days after the LHC was first switched on in September 2008, when a short circuit blew a hole in the machine and sprayed six tonnes of helium into the tunnel that houses the collider. Soot was scattered over 700 metres. Since then, the machine has been forced to run at near half its design energy to avoid another disaster.

The particle accelerator, which reveals new physics at work by crashing together the innards of atoms at close to the speed of light, fills a circular, subterranean tunnel a staggering eight kilometres in diameter. Physicists will not sit around idle while the collider is down. There is far more to know about the new Higgs-like particle, and clues to its identity are probably hidden in the piles of raw data the scientists have already gathered, but have had too little time to analyse.

But the LHC was always more than a Higgs hunting machine. There are other mysteries of the universe that it may shed light on. What is the dark matter that clumps invisibly around galaxies? Why are we made of matter, and not antimatter? And why is gravity such a weak force in nature? "We're only a tiny way into the LHC programme," says Pippa Wells, a physicist who works on the LHC's 7,000-tonne Atlas detector. "There's a long way to go yet."

The hunt for the Higgs boson, which helps explain the masses of other particles, dominated the publicity around the LHC for the simple reason that it was almost certainly there to be found. The lab fast-tracked the search for the particle, but cannot say for sure whether it has found it, or some more exotic entity.

"The headline discovery was just the start," says Wells. "We need to make more precise measurements, to refine the particle's mass and understand better how it is produced, and the ways it decays into other particles." Scientists at Cern expect to have a more complete identikit of the new particle by March, when repair work on the LHC begins in earnest.

By its very nature, dark matter will be tough to find, even when the LHC switches back on at higher energy. The label "dark" refers to the fact that the substance neither emits nor reflects light. The only way dark matter has revealed itself so far is through the pull it exerts on galaxies.

Studies of spinning galaxies show they rotate with such speed that they would tear themselves apart were there not some invisible form of matter holding them together through gravity. There is so much dark matter, it outweighs by five times the normal matter in the observable universe.

The search for dark matter on Earth has failed to reveal what it is made of, but the LHC may be able to make the substance. If the particles that constitute it are light enough, they could be thrown out from the collisions inside the LHC. While they would zip through the collider's detectors unseen, they would carry energy and momentum with them. Scientists could then infer their creation by totting up the energy and momentum of all the particles produced in a collision, and looking for signs of the missing energy and momentum.

One theory, called supersymmetry, proposes that the universe is made from twice as many varieties of particles as we now understand. The lightest of these particles is a candidate for dark matter.

Wells says that ramping up the energy of the LHC should improve scientists' chances of creating dark matter: "That would be a huge improvement on where we are today. We would go from knowing what 4% of the universe is, to around 25%."

Teasing out the constituents of dark matter would be a major prize for particle physicists, and of huge practical value for astronomers and cosmologists who study galaxies.

"Although the big PR focus has been on the Higgs, in fact looking for new particles to provide clues to the big open questions is the main reason for having the LHC," says Gerry Gilmore, professor of experimental philosophy at the Institute of Astronomy in Cambridge.

"Reality on the large scale is dark matter, with visible matter just froth on the substance. So we focus huge efforts on trying to find out if dark matter is a set of many elementary particles, and hope that some of those particles' properties will also help to explain some other big questions.

"So far, astronomy has provided all the information on dark matter, and many of us are working hard to deduce more of its properties. Finding something at the LHC would be wonderful in helping us in understanding that. Of course one needs both the LHC and astronomy. The LHC may find the ingredients nature uses, but astronomy delivers the recipe nature made reality from."

Another big mystery the Large Hadron Collider may help crack is why we are made of matter instead of antimatter. The big bang should have flung equal amounts of matter and antimatter into the early universe, but today almost all we see is made of matter. What happened at the dawn of time to give matter the upper hand?

The question is central to the work of scientists on the LHCb detector. Collisions inside LHCb produce vast numbers of particles called beauty quarks, and their antimatter counterparts, both of which were common in the aftermath of the big bang. Through studying their behaviour, scientists hope to understand why nature seems to prefer matter over antimatter.

"Unlike supersymmetry or the Higgs, there's no theory of antimatter that we can test," says Tara Shears, a physicist who works on the LHCb detector. "We don't know why antimatter behaves a little differently to normal matter, but perhaps that difference can be explained by a deeper underlying theory of particle physics, which includes new physics that we haven't found yet."

Turning up the energy of the LHC may just give scientists an answer to the question of why gravity is so weak. The force that keeps our feet on the ground may not seem puny, but it certainly is. With just a little effort, we can jump in the air, and so overcome the gravitational pull of the whole six thousand billion billon tonnes of the planet. The other forces of nature are far stronger.

One explanation for gravity's weakness is that we experience only a fraction of the force, with the rest acting through microscopic, curled up extra dimensions of space. "The gravitational field we see is only the bit in our three dimensions, but actually there are lots of gravitational fields in the fourth dimension, the fifth dimension, and however many more you fancy," says Andy Parker, professor of high energy physics at Cambridge University. "It's an elegant idea. The only price you have to pay is that you have to invent these extra dimensions to explain where the gravity has gone."

The rules of quantum mechanics say that particles behave like waves, and as the LHC ramps up to higher energies the wavelengths of the particles it collides become ever shorter. When the wavelengths of the particles are small enough to match the size of the extra dimensions, they would suddenly feel gravity much more strongly.

"What you'd expect is that as you reach the right energy, you suddenly see inside the extra dimensions, and gravity becomes big and strong instead of feeble and weak," says Parker. The sudden extra pull of gravity would cause particles to scatter far more inside the machine, giving scientists a clear signal that extra dimensions were real.

Extra dimensions may separate us from realms of space we are completely oblivious to. "There could be a whole universe full of galaxies and stars and civilisations and newspapers that we didn't know about," says Parker. "That would be a big deal."