We're crossing the border. Underpants Guy ducks behind the seat. "Forgot my passport," he grins sheepishly, through his rich man's face. Border guards won't care that Underpants Guy made a stack with his popular briefs. The man knocking on the window is a physicist. He says Underpants Guy should travel with him. His car has diplomatic plates. UPG brightens. He's out of our people carrier and into his upgrade. The border guards wave him through and salute.

Cern is special. Its physicists are ambassadors. It's like a small state. Ten thousand people work there. Iranians and Israelis pursue particle dreams together. So do Belgians. It attracts pilgrims. Politicians and pop stars visit. Mick Jagger will be coming. No one knows why. Perhaps he will refer to it in a throwaway remark. Perhaps he will be shut into the accelerator and be bombarded with protons for ten years.

Astroblogger has no doubt why he's here: dark matter. He used to work on the Hubble telescope. He's seen the shadow of dark matter moving across a cluster galaxy billions of light years away. Cern may reveal dark matter close up. Dark matter is made of particles that have never been detected. Dark matter makes up 25% of the mass in the Universe. Particles we can detect make up only 4%. What makes up the rest? Dark energy. I've boned up. Astroblogger tells me my understanding is "a bit sixties".

These concepts are not complicated by Cern standards. We are entering a zone which is weaponised to boggle.

Our first glimpse of the Atlas experiment is a vast white hole, like a tube for launching aircraft carriers into the Earth. A fenced diving board overhangs the 100m drop. As you stare down, your brain spins. If, at the same time, a physicist is telling you that a photon arrives on earth at the same time as it leaves the sun because it travels at the speed of light which is the speed of time so in fact a photon can be everywhere at once, you don't know whether your vertigo is physical or mental.

The Atlas chamber itself is a subterranean cathedral of physics. It is genuinely awesome. What you see is a bit like a colossal electric motor with a horizontal spindle. The spindle is the collider tube. It is perhaps a metre wide and for most of the 27km circuit that's all it is. But here, it has had a gargantuan outburst. Twenty-five metre high electromagnets built from melted Russian warships surround the tube and fill the space from floor to ceiling.

Flat muon chambers, like graphite doors, fan out from the tube. Flurries of smaller components and webs of bundled wires spray through the gaps. Each instrument is mounted with micron precision. And because that's more wayward than a batsman in Hastings trying to hit runs off a bowler in Scarborough, everything is swept and mapped by lasers to produce a true record of its position.

The experience is rapidly so impressive you start to salute each fact. The protons will make the 27km circuit 11,000 times every second. The accelerator tube will be one of the coldest places in the universe. We are making one of the coldest places in the universe. You have to salute that with both hands.

Almost all the collision events will be lost! Of the few you can detect, you can't even record 5%. But look! Cern has built the world's fastest computer. Its data storage will consume one good laptop every twenty seconds.

Reeling, we cross to a similar chamber called the Compact Muon Solenoid. It is here that the famous "God Particle" may emerge. And it is here that they really mug me with concepts. They try to soften the blow by claiming that physicists find it difficult to visualise extra dimensions too. That's easy to say when you're packing 26 of them. They've got the maths. They can pull down extra dimensions whenever they want their equations to balance. You just have to accept them. That makes you vulnerable. Your rationality dissolves.

Then someone hits you with the seething vacuum. You think a vacuum is empty space. Quantum theory says yes - but it is also full of spontaneous eruptions of energy. This virtual energy comes from nowhere. It does and doesn't exist. You can use the bit that does, so long as you pay it back. This beats sub-prime. A physicist called Polkinghorne says the quantum vacuum is the nearest analogy to God in the physical world. Then again, the physicist who is brainwashing me in the CMS says quantum theory is "probably bollocks".

At a meal afterwards, we babble. Will the collider suck us into a black hole? There's a website where some health and safety nut has calculated that Cern could be 18 times more lethal than death. Captain Underpants sees commercial potential in the proton. He wants to start a line of cosmetics. He actually wants people to rub their faces with massive nuclear fragments. Someone proposes a nightclub that is only slightly not called the Large Hadron Collider. Underpants laughs himself off his stool.

We have been subject to a powerful charisma. Cern combines deeply mystical particle theory with a gorblimey cock-in-the-turbo Clarksonism. UPG pops up from under the table like a meerkat. "Hey - reckon I could get Modonna to fuck a proton?" To our pulverised minds all things are horribly possible.

· Chris Morris is a lapsed scientist and is currently making a comedy film about British jihadis

· This article was amended on Tuesday July 15 2008. We claimed that the LHC will be the coldest place in the universe. The super-conducting magnets are cooled to 1.9 degrees above absolute zero (1.9K or -271.3C), but some low-temperature physics experiments can achieve temperatures of one-billionth of a degree above absolute zero. This has been corrected.