The governing body is accused of giving preferential treatment to clubs in rugby's heartland of NSW, ACT and Queensland by secretly enacting a plan called "Winning Rugby", without consulting the Victorian club.
The axed club is seeking $30 million in damages and to cover debts after it was booted from Super Rugby in May 2024.
But RA told the Federal Court on Wednesday the Rebels' pleas of ignorance about "Winning Rugby" were undermined by club president Paul Docherty.
In an affidavit, Mr Docherty said a proposal to merge the club with the New Zealand-based Moana Pasifika was supported by the Rebels board, RA's barrister Tony Bannon said.
"The board requests RA accelerate the commencement of the restructuring of the Rebels with Moana Pasifika to become the Melbourne Pasifika Rebels," Mr Bannon quoted from Mr Docherty's affidavit.
Mr Bannon said a proposed game for the 2025 British and Irish Lions tour against a Melbourne Pasifika club would not have been suggested had the club not been consulted on the merger.
Rebels barrister Bernard Quinn previously argued RA showed unfair preference to other clubs - the NSW Waratahs and ACT Brumbies - by assuming control but refusing to do the same for the Rebels.
But Mr Bannon said there was no proportionality in the financial positions of the three clubs.
The Waratahs had $3 million in debt and the Brumbies had about $2.4 million in debt when RA took over, compared to a negative position of $22 million at the Rebels, Mr Bannon said.
"(The Rebels argue) RA ought to have saved them from their own financial mismanagement," Mr Bannon said.
"Two or three million was not going to save the Rebels."
Mr Bannon pointed to communication between the club and the Victorian government asking for a $10 million grant to save the club as evidence it was not seeking to rely on RA.
The Rebels argued the governing body allowed them to collapse despite having a contractual obligation to maintain five Australian clubs in Super Rugby.
"If you let a club go, you have a breach of the obligations in the agreement with New Zealand Rugby," Mr Quinn said.
He claimed Mr Docherty was close with RA's then-chair Hamish McLennan and had agreed on the need for five domestic clubs in the months before the collapse.
Mr Docherty, who declared bankruptcy in 2025, is expected to give evidence in the three-week hearing.
In a final plea to resolve the lengthy proceedings, Justice Cameron Moore urged the two sides to extend an olive branch.
"It's not too late to resolve these proceedings ... millions of dollars will be (saved)," Justice Moore said.
The hearing continues.
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