In the end it came down to a choice between the Taoiseach, Mr Ahern, and the deputy from Mayo, Ms Beverley Cooper-Flynn.
After more than four hours of debate the Fianna Fail parliamentary party voted overwhelmingly in favour of the course of action advocated by their party leader and last night voted Ms Cooper-Flynn out of the parliamentary party.
However, even those annoyed by her temerity in bringing the issue so far acknowledged she turned in a sterling performance in defence of herself. But it was not enough.
Ms Cooper-Flynn's fate was sealed yesterday morning when the Taoiseach, Fianna Fail ministers and the Government Chief Whip, Mr Seamus Brennan, had a meeting and drew up the motion saying the party whip should be withdrawn.
The motion said that while acknowledging that Ms Cooper-Flynn was entitled to exhaust all rights of appeal in the courts process, "considered that it is in the best interest of the party and the work of the Government, that pending the final outcome of any appeal she may pursue, the Fianna Fail whip be withdrawn from the deputy".
There were no punches pulled yesterday. According to one TD, she had openly defied the Taoiseach and he did not like it. "He takes the softly-softly approach to begin with but she stuck her two fingers up to him and then stuck out her tongue. He doesn't like that."
During the parliamentary party meeting yesterday morning, Mr Ahern left to have a half-hour conversation with her. They were subsequently joined by Mr Brennan and the party chairman, Dr Rory O'Hanlon, who she had refused to meet the day before.
The Fianna Fail legal adviser, Mr Rory Brady SC, was in Heathrow, waiting for a flight to France. It was agreed, following a request from Ms Cooper-Flynn, that the meeting would be adjourned to allow Mr Brady and her legal representative, Mr Garrett Cooney, to speak on the telephone.
After a 3.30 p.m. restart, the motion was put to the meeting. Its proposer, Mr Brennan, spoke and was followed by the seconder, the Minister for Foreign Affairs, Mr Cowen.
In his address, Mr Ahern said that while no judgment was being made on guilt or innocence, the jury's decision was not something he could ignore. The action was necessary for the sake of the party and unless it happened he would keep facing questions and criticism in the Dail, the business of Government would be interrupted, and he also had to consider public opinion.
Ms Cooper-Flynn got to her feet and spoke for more than 40 minutes. Even those who believed she was foolish to have brought matters so far said she was very impressive. "It was a sterling performance," said one.
She outlined her reasons for taking the case, gave her insight into some of the things that went on behind the scenes during the seven weeks, including reading from some of the transcripts.
She passionately pleaded her innocence, saying she had not encouraged anyone to evade paying tax and that she was entitled to the due process. The motion would be prejudicial to any possible appeal she might make.
About 40 people spoke over the four hours. Over half of those said she should put the party first and resign, according to Dr O'Hanlon. Many said they found it a traumatic but necessary experience. They wished her well in an appeal if she decided to take one but told her that for the sake of the party she should resign from the parliamentary party.
About seven people spoke against the motion, including, Wexford TD Mr John Browne, Dublin TD Ms Marion McGennis and Cork TD Mr Batt O'Keeffe. A speech by Co Clare deputy Mr Tony Killeen, who himself was expelled over his disagreement with Government policy on ending the Shannon stopover, was said to have influenced many deputies.
At one point, Ms Cooper-Flynn proposed an amendment to the motion to give her more time. It was seconded by Laois-Offaly TD Mr John Moloney, but later he too said she should reconsider her position.
Just before Mr Brennan's motion was taken, Ms CooperFlynn addressed her colleagues again, reminding them of the importance of what they were about to do and the impact it would have on her. It was another moving contribution, according to one, but not enough.
A secret ballot was ruled out and a show of hands was taken, while a visibly emotional Ms Cooper-Flynn looked on.
According to Mr Brennan, there were just over 70 people at the meeting and 68 voted in favour of the motion. It was, said one TD, a simple choice in the end. "It came down to voting for Beverley or the Taoiseach, that's how it went."