Linda Cook – the Shell executive once tipped for the top job – has resigned unexpectedly, forfeiting an £800,000 bonus in the process.

Ms Cook worked for the Anglo-Dutch giant for 29 years, most recently as executive director of the company's gas and power division, which includes Shell's fast-growing liquefied natural gas unit.

Her departure comes just as Shell is expected to announce a major restructuring that could see her division merged with the company's other main unit, exploration and production, a move that Ms Cook is believed to have opposed.

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She was also one of a number of internal candidates in the running to succeed the outgoing chief executive, Jeroen van der Veer, and, if successful, would have been the first female boss of a major oil company.

But she was beaten to the post by the chief financial officer, Peter Voser, and will instead step down at the end of this week, although she will retain an advisory role at the company until a successor is found.

By handing in her notice, Ms Cook has given up the £800,000 loyalty payment due to unsuccessful applicants who remain with the company for a further three years.

Mr Voser, who will take over next month, is putting together his management team. The company says that Ms Cook's departure is by mutual consent.

Mr van der Veer said: "I am most grateful to Linda Cook for her many important contributions to the success of our company." But City gossip suggests that Mr Voser and Ms Cook do not get along.

The surprise departure of a high-profile executive is just the latest of Shell's problems. Last week, 59 per cent of shareholders voted down the directors' remuneration package at a fractious annual general meeting and called for millions of pounds worth of bonuses to be repaid.

The row escalated over the weekend as a number of large investors demanded the resignation of Sir Peter Job, the chairman of the remuneration committee that has signed off discretionary share awards for executives despite the company's failure to meet targets on shareholder returns.

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Even worse than the pay scandal is the start of the New York court case accusing Shell of complicity in the death of Ken Saro-Wiwa, the environmental activist executed by the Nigerian government in 1995.

The civil trial was due to start today but was last night delayed, according to the Centre for Constitutional Rights, which is a representative for the plaintiffs. Shell denies any involvement in the killing of Mr Saro-Wiwa, but whichever way the trial goes it will not be good news.

One of Mr Saro-Wiwa's main cause célèbres was gas flaring in the Niger Delta. Energy companies, particularly Shell, have been flaring gas in Nigeria for more than 30 years. The company has a "flare down" programme, but has refused to provide a timetable.

Green groups claim that flaring in Nigeria emits as much carbon dioxide into the atmosphere every year as 18 million cars and have branded Shell as the most carbon-intensive of the big oil companies.

The Saro-Wiwa case will refocus attention on the issue, says James Marriott, from the lobby group Platform.

"The oil companies would never flare gas like this in continental Europe – it would be laughable."