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Steven Deans believed he was being treated as the "enemy within" after 25 years of working at the plant, according to Unite.
Mr Deans accused the company of leaking emails to the media to "smear his reputation", in his resignation latter to Ineos.
He told the Unite meeting: "The hurt to my family is unforgivable and I will not allow management to take away my dignity and self-respect any further."
The union said it is considering "what steps can be taken on Mr Deans' behalf" without diminishing its commitment to the survival plan workers signed with Ineos last week.
Steven Deans, the Unite union's representative at the Grangemouth refinery in Scotland, was at the centre of a dispute which led to the refinery's bosses threatening to shut down the whole site.
He has now resigned a day before he was due to meet his employer, Ineos.
Mr Deans was also chairman of the Labour party in nearby Falkirk, and was accused of trying to install Unite's choice as Labour candidate for MP. ITV News Deputy Political Editor Chris Ship reports:
Ed Miliband has been urged to consider reopening Labour's inquiry into allegations of candidate-selection fixing in the Falkirk constituency.
Commenting on today's resignation of Grangemouth union official Stevie Deans, Conservative Party chairman Grant Shapps said:
Grangemouth union official Stevie Deans resigned after learning the findings of a disciplinary case against him, said refinery operator Ineos.
Deans was investigated by the company following his involvement in the row over the selection of a Labour candidate in the Falkirk constituency.
Stevie Deans, the Unite union official at the centre of the Grangemouth dispute, has resigned from his job at the plant, owner Ineos has confirmed.
Prime Minister David Cameron welcomed the deal to keep Grangemouth open, during a press conference in Brussels.
Jim Ratcliffe, chairman and chief executive of Ineos Group, described today's news as "a victory for common sense".
"Grangemouth is the powerhouse of the Scottish economy," he said. "It now has a fighting chance of upholding this crucial role into the future.
"Obviously today's news is tinged with sadness," he continued. "Decent men and women are being asked to make sacrifices to hold on to their jobs but the clear wish of our members is that we work with the company to implement its proposals."
Scotland's First Minister Alex Salmond has commended workers at the Grangemouth refinery for making a "substantial sacrifice" in order to keep the plant open.
He said the agreement was a "great achievement" by a range of different parties with an interest on the plant's future.
David Cameron said he would "congratulate everybody involved" in keeping the Grangemouth petrochemical plant open.
John Convery, a manager at Grangemouth, described the last few days as "hellish"
"Myself and my colleagues, and all of our families, have been staring into the abyss," he said.
He added: "We'd just been paid but we didn't know if we were going to get another pay cheque again. We were told that the company we work for was going into liquidation and we didn't know if we were going to get any redundancy or what was going to happen to our pension ...
"There was a lot of relief and a lot of emotion in there, we're relieved that we've still got a job."
Latest ITV News reports
Grangemouth owners Ineos are in last ditch talks with the workers' union, but the workforce is just one of the problems facing the plant.
Thousands of jobs are under threat after a dispute over conditions led to a shock decision to close the petrochemical site in Grangemouth.