In that year, an introduction to Charles Watson-Wentworth, the Second Marquess of Rockingham – the Whig politician who was to become a two-term Prime Minister – of Wentworth Woodhouse, near Sheffield led to the commission of four "large as life" paintings.

Whistlejacket, a portrait of an Arab stallion,was hung in its own room at Wentworth, Lion attacking a horse and Lion attacking a stag hung at the Marquess's London home, and Scrub, a bay racehorse was rejected, although there's no record of the reason for this.

There's no evidence that the relationship between artist and patron had soured, and later the same year Stubbs did a smaller painting of the 14-hand Scrub, with Rockingham's jockey John Singleton (the Lester Piggott of his day) on his back. At the end of the horse's racing days, the stallion was given to Singleton, and the two are buried at Givendale on the Halifax estate in East Yorkshire.

Whistlejacket stayed in the Rockingham family and led a cosseted life for more than two centuries until the marquess's descendants sold the painting to the National Gallery in 1997 for a sum thought to be between £14m and £20m. It's one of the gallery's major tourist attractions.

Scrub had a much more chequered career. Initially it remained in Stubbs's studio until his death in 1806, and in 1898 turned up in the collection of the Fifth Earl of Rosebery, from whom it passed down to the Earl of Halifax, taking pride of place in his private library until it was removed for major restoration 18 months ago. The only time the two immense paintings (both just under nine-foot square) could have been in the same room until a few days ago was when they were being painted.

Scrub has until now never been seen in public, but a friend of Lord Halifax's, York-based art adviser Sir Nicholas Brooksbank, had a burning desire to see the two great horse paintings "nose to nose" in an historic artistic event.

He smelled an opportunity with the removal of Scrub for restoration by Canaletto, Holbein and Stubbs expert Viola Pemberton-Piggot. If the two canvases were ever to hang side by side it was before Scrub disappeared back through a window into Lord Halifax's home. Brooksbank took his friend, the Leeds-based property developer, millionaire and art collector Kevin Linfoot, to see Whistlejacket at the National Gallery and laid out his plan. Linfoot agreed to bankroll the project, so long as the show happened in Leeds.

The cost of making it all happen was estimated at £150,000. Of course, all this was planned a year ago, before the credit crunch began to bite.

Six weeks before the opening, costs had escalated and at the same time Linfoot's business was suffering thanks to the declining economy. Lumiere, his biggest and most prestigious development was put on hold, and he had to put a cap on his sponsorship, leaving Brooksbank to raise funds elsewhere.

When 100 guests gathered at Leeds Art Gallery for the gala opening in aid of Macmillan Cancer Support the other night, it was difficult to tell who was the more relieved that somehow the dream had been realised – was it Brooksbank or Viola Pemberton-Piggot, the restorer who, along with colleague Anna Sandén, had lived and breathed this painting for so long?

All involved in the enterprise agreed that the effort had been worthwhile. Kevin Linfoot felt the accessibility of Stubbs's work would trigger visits to the gallery by people who might not normally consider art as their natural turf; Lord and Lady Halifax marvelled at how their beloved painting was now revealed in its true colours thanks to painstaking care and expertise; Brooksbank seemed almost dumbstruck with excitement that he'd pulled off this artistic coup.

The self-effacing Viola Pemberton-Piggot gave a fascinating insight into the art of Stubbs from the unique perspective of one of very few people equal to the task of removing layers of poorly applied and inappropriate over-painting by previous "restorations".

Her efforts revealed shrubbery in a corner of the canvas that even its owners had never noticed. Once restored, the tint of the sky was entirely different. A tree which had been dark green was uncovered in all its coppery glory.

"I wasn't exactly overjoyed at the idea of doing this restoration," said Pemberton-Piggot. "So much work needed doing to it, and I could see it would use up one's entire life."

The story goes that after its rejection by Rockingham, the canvas was folded, rolled up like a carpet and was somehow crushed during a sea voyage to India with a consignment of other paintings. On arrival it was so damaged that it was sent straight back.

Stubbs himself performed a restoration, but later bouts of remedial work were more heavy-handed, and, rather than solving problems, simply obscured the beauty of the original.

Using various solvents to remove unwanted layers, then matching Stubbs's paint tones, Viola and her team worked to take Scrub back to his original glory, his tail swishing and haunches rippling in various hues of bay over the artist's unusual yellow ground.

"Until recently experts did not think the landscape around Scrub was actually Stubbs's own work. It did not appear to be in his style, with dense, deep greens and heavy dark clouds. In a sense they were right, because people were seeing overpainting done by others. What we see now is what was intended by the painter, and that is very satisfying."

She may be exhausted by Scrub but there's not much rest ahead for the in-demand restorer – Viola Pemberton-Piggot has a cupboard full of other Stubbs works awaiting her tender loving care.


Whistlejacket and Scrub: Large as Life is at Leeds Art Gallery, The Headrow, Leeds, until November 9.