Alex Salmond’s lawyer has told jurors at the former first minister’s trial that the entire sexual assault and attempted rape case is “murky” and “smells bad”.

Gordon Jackson QC, Salmond’s defence advocate, told the jury of nine women and six men in Edinburgh they had to use their “rational minds” and acquit the former first minister of all 13 charges against him.

In his closing speech to the jury on Friday, Jackson said a “scary” pattern had emerged with all the allegations, some of which dated back 12 years. There were no direct witnesses to the alleged assaults, which include a charge of attempted rape and one of intent to rape.

Jackson apologised to the jury for saying earlier in the trial that some of the alleged offences were trivial, but said inconsistencies and contradictions cropped up repeatedly in the testimonies and evidence. And, he alleged, there were signs some of the charges were orchestrated.

“This comes out of a political bubble with no real independent support of any kind. I said already it smelled and I don’t apologise for that one bit,” he said, summing up the defence case after the two-week trial.

“I don’t care if you like him or you don’t like him. He was the Marmite man but I know he’s entitled to the law’s protection. He’s entitled not to be convicted of anything unless there’s clear evidence.

“It’s the same pattern all of the time,” he said, arguing that matters not deemed serious at the time had been inflated to criminal charges later. “All the time – I can’t say that strongly enough – it is the same pattern over and over and over again. It’s scary.”

Salmond, 65, from Strichen, Aberdeenshire, is charged with an attempted rape, an intent to rape, nine sexual assaults and two indecent assaults involving nine women, all of whom are current or former Scottish government officials, or a Scottish National party politician.

Many of the offences allegedly took place at Bute House, the first minister’s official residence in Edinburgh. Salmond was originally charged with 14 offences but he was formally acquitted of one charge, a 10th sexual assault, on Monday after the prosecution withdrew the charge.

Before sending out the jury to deliberate, the judge, Lady Dorrian, told them to weigh up the evidence before them very carefully.

There were three verdicts available to them: guilty, not guilty or not proven – a Scottish verdict which also means an acquittal. The jury were able to amend the charges if they felt the evidence did not support the wording on the indictment.

On Thursday, Alex Prentice QC, for the prosecution, had told the jury Salmond was a sexual predator who exploited his power to prey on younger, subordinate women. “This case isn’t about a plot or political conspiracy,” Prentice told them. “This is about a powerful man who abused his power to satisfy his sexual desires with impunity.”

However, Jackson dismissed Prentice’s argument. He said the inconsistencies and contradictions at the very least raised doubts the allegations were true. He told the jury that if they had any hesitation about the truth or accuracy of the charges, they had to acquit.

You cannot take a risk “with his life or anybody else’s life … If you accept any of these things is a criminal matter, you need to be satisfied to that high, high standard.

“If you thought they were probably established or more likely than not established … you would acquit him.”

He said the crown’s claim that Salmond has sexually assaulted one official with an intent to rape had not been proven. “It’s a hell of an allegation,” Jackson said. “It’s a very, very big allegation to make in the high court.”

Allegations by witness H that Salmond had attempted to rape her at Bute House were disproved by a witness in court who said H was not there, he suggested. Although a celebrity, who cannot be named for legal reasons, gave an interview by Skype to the police, that person was not under oath and the defence could not cross-examine him.

The celebrity said H was there but that was “totally contradicted” by another witness who was cross-examined in court, Jackson argued: she knew H well and denied she was at the dinner or even in the building.

“If you had doubt at all she was there, that is the end of the charge. He cannot be guilty if she wasn’t there,” Jackson told the jury. Jackson implied H wanted revenge on Salmond because he thwarted her professional ambitions. “This is a murky, murky world we live in.”

Jackson alleged that witness A, a senior Scottish government official who accused Salmond of repeatedly kissing and touching her without permission in Glasgow in 2008 and fondling her body in a nightclub in Edinburgh, had tried to orchestrate some of the charges.

“That stinks,” he said. “It absolutely stinks.”

Witness A contacted at least four of the complainers, all serving or former officials, before Salmond was charged, Jackson told the jury. They used a WhatsApp group.

A fifth complainer, a senior politician, had refused to take part in those conversations because she felt it was inappropriate, the jury heard. “There’s something that doesn’t smell right in the whole thing and you’re supposed to be satisfied beyond reasonable doubt” that Salmond’s behaviour was criminal, Jackson argued.

The jury retired to begin its deliberations shortly before 2pm.