In 1993, Clarke designed sets for Dutch National Ballet’s The Ruins of Time in Amsterdam, choreographed by Wayne Eagling, with music by Tchaikovsky. This performance was a tribute to the dancer Rudolf Nureyev, who had died of complications from HIV/AIDS earlier that year, and whom both Eagling and Clarke had known. Clarke designed sets for a second version of the ballet in 1997, also choreographed by Eagling with the Dutch National Ballet.

Each ballet included a set with a backlit stained glass artwork. In 1993, this was the Chelsea Window. In the second ballet, in one set, the stage was overlooked by a sample panel for Norman Foster's Al-Faisaliah Center. In 2018, Clarke explains another set, which was a tribute to those lost to the epidemic:

'Each figure is somebody of my friendship or acquaintance who had died of AIDS, and during one of the scenes, which started with the full corps de ballet, they were all lit when the scene began until, one by one, the spotlights went off and the dancers disappeared, ‘till the only face left was Rudolf’s, and as the light on his face dimmed the last ballet dancer disappeared into the stage floor.'