"Right across the site we found deposited human remains." It is not the sort of thing you hear every day. If I found a medieval cemetery, I do not think I would be as calm and collected about it. But for Ross Cameron of Addyman Archaeology, it seems to be a common occurrence. Over the past few months, Ross has been the site director on the archaeological dig at Old College. Beneath the gravel of the quad his team have found skeletons, a medieval church, a burial ground and have come tantalisingly close to lodgings where murdered Lord Darnley spent his last drunken evening.

Henry Stuart, Lord Darnley, King consort of Scotland, was the arrogant, alcoholic but evidently dashing second husband of Mary Queen of Scots. "One look at Darnley’s shapely calves," writes Simon Schama, "and Mary decided she must have him." Married in 1565 at Holyroodhouse, Darnley moved from his Yorkshire birthplace to live with Mary in Scotland. In no time, she was pregnant.

However, in Darnley’s eyes at least, there seems to have been some question as to the paternity of the child – who, as it turned out, would be the next King of England. Suspecting Mary’s Italian aide, Darnley murdered him in a jealous rage at Holyroodhouse, after which he lost it completely, turning more than ever to his beloved bottle. Mary, mildly irritated that her loving husband had stabbed her friend 56 times while she tried to eat her tea, thought she’d branch out and get some new mates. Bring in slimy James Hepburn, 4th Earl of Bothwell.

On the night of February 10th 1567, Darnley and his valet were found dead in the grounds of a church, thought to be close to modern day Old College. The house they had been staying in had been blown up, and they had managed to escape, only to be strangled when they got outside. Unsurprisingly, Bothwell was implicated – as was Mary.

"Looking from the main entrance of Old College, our dig has shown that there was a church at the back left corner of the site" says Ross. "It was there from about the 13th to the 16th century." Current thinking is that this church was Kirk o’Field, the collegiate church of St Mary in the Fields, which neighboured Darnley’s lodgings. "In the far right corner, there are the remains of the collegiate hospital. We think that a medieval cemetery probably ran between the two, right down to somewhere close to the current Old College entrance, and it is from this that we’re getting all the bones. From midway down the site we’ve found about 59 skeletons. Scarily some of these were only about 20cm from the surface. Just think how many times you’ve walked over there completely unaware of that. Basically everywhere we dug, we found human remains."

Surely when they built Old College, they were aware of the skeletons? "Builders in the past must have known these remains were there. We found hardcore 30cm deep, and then some skeletons at 20cm, so the builders must have just shovelled the bodies back into the ground, without removing them. There are also various services going through the site, and some of these skeletons have just been chopped in two by these pipes." Ross points out that "it is not always easy to spot human bones", commenting that it was probably a mixture of laziness, looser legal requirements and simple ignorance that meant so many bones remained beneath Old College.

The team used a technique called map regression, where overlays of historical maps are placed over their modern equivalents to help locate the buried buildings. "The old maps and drawings have been surprisingly accurate" said Ross. "I suppose you’d expect that, with the site having been occupied by the University since 1583." The archaeologists had some idea where the Kirk was, aware that Edinburgh’s mid-16th century Flodden Wall made a special diversion to include the church in the defences. Parts of the Flodden Wall can still be seen along Drummond Street and down to the Cowgate – so called because it was a gate in the wall for cattle.

So what about Darnley? Has the dig got us any closer to discovering what happened on that night 443 years ago? "The building the murderers exploded was one of the outbuildings of the church, which then went on to become the Provost’s lodgings and then the first Edinburgh University Principal’s house. Unfortunately we’ve not found any remains of this building, but we do now have a good idea where it is. We think it is probably underneath the south east corner of the current Old College building. We are within a couple of metres of it, but short of undermining the present building, we are unable to get at it."

Following Lord Darnley’s murder, his father Matthew Stewart, the fourth Earl of Lennox, began a campaign to get Mary convicted. Many thought it just that little bit too convenient that Bothwell appeared on the scene and married the queen, just as Darnley was handily strangled. However, Addyman Archaeology states that "although we’ve got an expert studying the bones, we’ll never be able to identify Darnley."

So when the quad development is finished, its new grass lain, why not take a stroll and wonder what lies beneath?