The hunt for the universe's tiniest particles has required the construction of the largest and most sophisticated machine ever built.

It is an irony I can't help but notice as I travel the 17 miles around the Large Hadron Collider (LHC), the underground loop of tunnels, caverns and computer monitoring stations which saddles the Swiss-French border a few miles north-west of Geneva.

Forget the protons, neutrons and electrons of high-school science – here beams as thin as a human hair yet loaded with trillions of protons are smashed together at virtually the speed of light to observe the debris of even tinier particles, equivalent to the make-up of the universe one-billionth of a second after the Big Bang. Like a matryoshka doll, what's thrown out gets smaller and smaller – and increasingly bizarre. From a top quark – a sub-atomic particle which weighs as much as a gold atom – to mesons, which oscillate between matter and antimatter states.

It is nine months since CERN, the European Organisation for Nuclear Research and the body in charge of running the LHC, announced it was almost certain it had observed the Higgs boson, a major leap towards unlocking one of physics' most enduring mysteries: why mass exists.

The idea of the Higgs, specifically the Higgs field, was put forward 50 years ago by Edinburgh particle physicist Peter Higgs to help resolve this "missing link" in physics.

Dr Victoria Martin, a physicist at Edinburgh University and a member of the LHC's Atlas project, one of two experiments searching for the Higgs, says: "What Peter Higgs actually predicted is not the Higgs boson. What he predicted was something called the Higgs field. You can think of it as a bit like a magnetic or electromagnetic field. A magnet causes a magnetic field, and an electromagnetic field is caused by something like a TV mast, but the Higgs field doesn't need a source – the hypothesis is that it is just there, throughout the universe, everywhere."

Like treacle, this field bogs down some particles – making them heavy – while other, lighter particles zip through untroubled.

Without it the universe would be nothing more than a cloud of aimless particles and nothing – from stars to human beings – would ever have existed.

Yet despite last year's discovery, arguably the most significant breakthrough this century and one of the most important since Einstein's theory of relativity, the mood among the scientists is that their work is only just beginning.

If you've watched TV documentaries on the LHC, you will have seen the CMS detector, or compact muon solenoid. Undoubtedly the most visually awesome of the four detectors, it is a gigantic round device located 246ft below ground and filling a cavernous space from floor to ceiling with its 82ft diameter. There are walkways halfway up to the side, and below a team of workmen wrestle to assemble what looks oddly like a coat rack.

"Guess who does the plumbing on it?" our guide asks, pointing to the detector. "The Poles." It's an amusingly mundane link between the colossal and the domestic.

Like Atlas, the primary aim of CMS is the quest for the elusive Higgs. Despite some 40 million collisions per second, a Higgs boson is created only once every couple of minutes – tantalising evidence of the Higgs field, which vanishes almost instantly.

"Finding the Higgs – we knew what we were looking for and how to look for it," adds Dr Newbold, one of the lead researchers. "Everything from this point onwards is really unknown."

The LHC has been shut down for repairs and upgrades ahead of 2015 when the power levels will be cranked up and the proton load increased, generating even more collisions. It looks rather like a high-tech factory – oversized pipes are covered in tinfoil and a mass of wires; in control rooms sit dozens of computer screens, one on top of the other, used for monitoring collisions and sifting through data. There's an empty bottle of champagne in one room, a remnant perhaps of the Higgs boson celebrations.

Power has been kept at a relatively low level after the LHC's much-publicised breakdown in 2008, nine days after launch. The hope is that the improvements, by enabling power to be ramped up, will allow physicists to say conclusively that they have found the Higgs boson.

However, other puzzles have barely begun to be unravelled and one of the tests ahead is explaining why there is so little antimatter left in the universe. "It's an amazingly exciting time," says Dr Aiden Robson, an Atlas project researcher and particle physicist at Glasgow University. "When I started working in this field nobody knew about CERN or particle physics, but now there's a lot of interest.

"Being able to say we have definitely found the Higgs boson would be hugely significant because it tells us something significant about the fabric of the universe. But there are all sorts of things the [particle physics] standard model doesn't explain, like why we're here at all.

"When the universe formed, you would have expected as much matter as antimatter to have been created, but there wasn't. A tiny bit of matter was left over and it's that imbalance which stopped everything from blowing apart – otherwise there would have been nothing but microwave radiation. But we don't know why that happened."

It is worth making clear that while the vast majority of coverage surrounding the LHC since it went live in September 2008 has focused on the Higgs boson, this is not the sole interest of the thousands of researchers based here and analysing the data worldwide.

While the Atlas and CMS detectors are primarily interested in the Higgs, scientists are also working to unlock the mystery of antimatter and others are studying the little-understood "strong force", which glues quarks together to form protons, neutrons and hadron particles.

Antimatter is probably best known as a weapon-of-choice in science fiction, vaporising foes in a single blast. In reality, there is so little antimatter left that it would take almost the lifespan of the universe – almost 14 billion years – to generate enough of it artificially for a single blast from a typical sci-fi film weapon (if such a device were even possible) and the effect would be more like a nuclear bomb exploding.

As the name suggests, antimatter is material composed of antiparticles, which have the same mass as particles of ordinary matter but an opposite charge – for example, an anti-electron carries a positive charge.

Deep underground, in a room reminiscent of the set used for the finale of Terminator 2: Judgment Day but with more primary colours and minus the lakes of molten metal, fragments of antimatter thrown up as particles are blasted through layers of silicon, metal and carbon fibre and analysed.

Dr Lars Ekland, a Glasgow University physicist, says: "We hope we will start to find a crack in the standard model that will help us dig down and uncover some of the mysteries around antimatter."

Even less is known about dark matter and dark energy – theories so new they didn't even appear in a typical university physics syllabus 10-15 years ago.

Dubbed "science's little embarrassment", it refers to the fact that only 4% of the universe is known. The remainder is believed to be made up of dark matter and dark energy which scientists concede they don't understand.

Dark matter was first suspected in the 1930s when scientists noticed anomalies in the motion of stars which seemed to contradict the amount of matter in the galaxy – that is, they were moving more slowly than they should, suggesting some invisible matter was exerting a gravitational pull.

Dark energy, thought to make up close to 70% of the universe, is an even bigger mystery. It appears to be responsible for accelerating the rate at which the universe is expanding, acting like an anti-gravitational force.

Dark matter and dark energy have never been seen and scientists have no idea what it is – only that it is out there. With the ongoing attempts of researchers at the Large Hadron Collider to find this holy grail of science, identifying the Higgs boson may yet be overshadowed. n