We encountered many spirits on our trip around Mexico, from the Aztec jaguars that screeched at us as we walked around pyramids, to the Mayan sun gods who beat down on us as we drove across the Yucatán peninsula — but none were as vexatious or mischievous as the invisible pig.

It may seem strange to invoke such a little beastie when writing about exuberant and exotic Mexico, but the mesmerising country has so many layers that although the swine flu alert was worrying, it showed the country in a different light. The unpredictable pig also limited our trip, its shadow falling on all tourist activities, but the threat has now been downgraded and the trouble it caused is the very reason to book now and go back in droves.

I went with a friend, with an ambitious plan to drive from the pulsing capital city, south through jungles and mountains of mystery, then east across the Yucatán peninsula, not stopping until we hit the Caribbean coast.

We had pored over maps and compared notes. But we should have known: Mexico does things on its own terms. You can avoid hurricane season and ignore overcooked stories about road-side bandidos, but if you really want to cross Mexico, you either need time, or plane tickets.

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BACKGROUND

• Grabbed by the Mariachis in Mexico City

• Mexico's mass butterfly migration

• Los Cabos, Mexico: this year's star

• Ask our expert: Mexico's 'Day of the Dead' festival

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• City style: Mexico City

• Gringo's peyote trip in Mexico

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We started at an altitude of 2,240m, in the city of nine million that was built on the plateau of a lake, and is gently sinking. Mexico City (or just “México”, as it’s called) has coped with earthquakes and revolutions, so swine flu was a mere blip — but it did clear the traffic-choked avenues, empty churches on a Sunday and shut archaeological sites.

What it showed us were proud, practical and kind people, spirited in the face of a global menace, when the world seemed to be pointing a finger at its trembling livestock. It was the start of an itinerary filled with people, rather than places.

Just as our guide, José Luis, remained sanguine, people seemed to be taking the shutdown in their stride. Where giant churches, such as the Basilica of Guadalupe that draws millions in the time of pilgrimage, were draped in tape and partly shut down, the vibrant gardens of Xochimilco were busy with families, gliding down the canals in Trajinera boats (think of covered, brightly coloured punts, named Laurita and Conchita), with irrepressible mariachi bands commandeering boats and playing for a fee, and smaller boats nipping in and out offering food, drinks or flowers. Here we suddenly got a glimpse of what the roads might have been like had we arrived a week earlier.

Our tour guide sped us around in his car, slightly bemused by our trepidation. He escorted us from the wide avenues near our hotel to the artistic quarter of Coyoacán and the empty stadium of the Ciudad Universitaria — normal capacity 75,000, that day, 0. It wasn’t just the religious who couldn’t worship. We still felt the footfall of the tens of thousands: despite the sense of quarantine, it was easy to see what non-H1N1 Mexico would have been like.

The one we began to make out in Mexico City was a joy — from its epic history, to its energy and abundant nature. Yes, parts of the country are dangerous, some are florid, but some are so hypnotically beautiful that you’ll be tempted to tear up your return ticket.

The city’s main square and historical centre, the Zócalo, seemed populated by nervous tourists and masked police, but the sheer scale spoke of the missing masses. This was where Mexico old and new fused — with government and church buildings overlooking one of the world’s largest squares, the scene of riots, demonstrations and celebrations alike, all above the heart of the old Aztec city.

Here, Moctezuma II, the last of the elected Aztec emperors (Montezuma is an anglicised corruption), met the Spanish leader Hernán Cortés in 1519. Just off the square is the ceremonial site of the Templo Mayor that was built over by the Spanish conquerors and lay undiscovered until 1978, when a workman hit the remains and struck historical gold.

Did the brave emperor, hero of a sophisticated, bloodthirsty civilisation, capitulate to the Spanish or make an error when he welcomed them into the city? You stand on the site and wonder at the stripping down that took place, the clash and crunch of civilisations, the destruction that gave birth to such a place as Mexico City.

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