When the Royal Lyceum Theatre in Edinburgh announced the resignation of its artistic director Mark Thomson last week after twelve years at the helm, there were some who thought Thomson's decision was in response to Scotland's arts funding quango Creative Scotland's potentially damaging 17% in the theatre's regular funding.

Here, after all, was one of the country's leading rep companies who, as this season's productions of Brian Friel's Faith Healer, Tony Cownie's new take on Goldoni's The Venetian Twins and Thomson's own boisterous production of Brecht's The Caucasian Chalk Circle (pictured) have proved, is at the top of its game.

This was confirmed by the news that the Royal Lyceum has been nominated for a record-breaking seventeen awards at this year's Critics Awards For Theatre in Scotland. The announcement too of the theatre's 50th anniversary season as a producing company has also set the country's theatre scene aflutter, with Thomson's opening production of Samuel Beckett's Waiting For Godot starring a dream team of Brian Cox, Bill Paterson and John Bett alone worth signing up for.

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The Lyceum's 2015/16 season also features productions of Arthur Miller's The Crucible and Conor McPherson's The Weir. There are co-productions with the Lyric Hammersmith on Tipping The Velvet, and the National Theatre of Scotland and Told by an Idiot for I Am Thomas, a new play about Moliere, Thon Man Moliere, by Liz Lochhead and a stage version of Homer's Iliad by Chris Hannan. With such a strong season, Thomson's departure following a typically fearless statement which declared Creative Scotland's decision to make the cut a "perverse punishment for acknowledged success" might appear to be connected. In truth, however, Thomson's departure has been in the pipeline for over a year.

"I'd already decided to go long before the funding cut," he says of the decision, "and it feels both liberating and scary, but with absolutely no sense of, oh, God what have I done? Whatever the arc of my time here has been, I do think that because of the sh**** thing that has happened to the company in terms of funding, it's not wrong for someone else to come in and think really clearly and unsentimentally about what this place could this be."

Sitting in the auditorium of the theatre he's called home for more than a decade, Thomson talks about just how special the theatre's fiftieth anniversary is.

"I've just recently passed through my fiftieth portal as well," he says, "and there's no doubt that invites a degree of reflection on what you've been, on what you are and what you will be, so I've entered the programme with that very much on my mind. It's not about looking back in a nostalgic way, because nostalgia has no place in theatre, but to be able to field someone like Brian Cox, who was in the original Lyceum company, and Billy Paterson, who was here in the sixties, that's the trumpet. That's what a fiftieth season should be about."

Thomson arrived at the Royal Lyceum in 2003 to take over from Kenny Ireland after running the Brunton Theatre in Musselburgh for several years. A new policy in East Lothian meant that the venue would no longer be a producing house, and, with Ireland departing the Lyceum after his decade-long reign, Thomson stepped up. Prior to that, the Livingston-born director had begun his professional directing career at Theatre Royal Stratford East and the Royal Shakespeare Company before moving back to Scotland.

In the time he has been in Grindlay Street, Thomson has directed over ninety productions, twenty-eight of which were world premieres. Amongst the latter were two plays of his own, including the award winning A Mad Man Sings At The Moon. As well as this, he has built up a core team of associate artists, with director John Dove working his way through Arthur Miller's canon, while Tony Cownie has concentrated largely on more comedic fare. More recently, Amanda Gaughan has demonstrated her directing skills on a big stage with Hedda Gabler, and looks set to continue next year with her production of The Weir.

Thomson put David Tennant on a big Scottish stage playing Jimmy Porter in a production of John Osborne's Look Back in Anger, just prior to him taking up his tenure as Dr Who. More recently Thomson packed out the auditorium for a brand new play by Ian Rankin.

Despite such successes, the cut came as a shock, and Thomson still isn't shy of saying what he thinks of it.

"I'm not sorry I said what I did," he says of his original reaction. "You can't be putting on plays like The Crucible and not say what you think, otherwise I'm a fraud. Very fundamentally, Creative Scotland's decision to cut us felt ill thought out. It felt like we'd become part of a numbers game that didn't relate to the quality of the work. I didn't feel like they had a vision for us other than to do it for less, and at that point I don't know what the conversation is. I don't know how to talk to them, because I don't know what they mean.

"It became very close to wondering if they want a company at all. It's a cut of over 200 grand a year, which is almost a third of our entire production budget. When you think the fabric is being damaged, not the garden, but the reason the house exists, you can't not say something."

As it is, the conversation that has occurred has enabled the Lyceum to function at the same level for this year and next, with a massive fund-raising operation necessary to make the third year in the theatre's funding cycle happen at all. By that time Thomson will be long gone, though doing what he genuinely hasn't a clue.

For the immediate future Thomson will be looking to cast Lucky in Waiting For Godot. Given that the role requires the actor to perform one of the lengthiest speeches in modern dramatic history, this will be no easy task. As he breezes into the theatre foyer, however, it's a task he clearly relishes.

"I don't want to be ten per cent less," he says. "That's what happens if you stay somewhere too long. I want to be a hundred per cent, but I feel quite freed about next year. It's oddly liberating, and doesn't feel at all sad for me. It's really exciting, and doesn't even feel like it's a last hurrah. I just feel like I'm coming into work really happy and positive, and that's okay, isn't it?"

Tickets for all shows in the Royal Lyceum Theatre, Edinburgh's 50th anniversary season are on sale now.

www.lyceum.org.uk