Lawyers for David Eastman told a jury Thursday that there are gaps in the Crown case that cannot be filled.
Defence counsel George Georgiou SC said that no amount of squeezing or pulling the puzzle pieces into place would show the picture the prosecution wanted them to see.
"There is simply too much that is unknown in this case, too much that is uncertain," he said.
He warned the jury that speculation, guesswork and conjecture had no place in the court.
At the beginning of his closing address on Thursday Mr Georgiou told the jury Mr Eastman was not guilty of murdering Colin Winchester on January 10, 1989, and that he had not bought the murder weapon.
That the man who sold the gun used to shoot the assistant commissioner did not identify Mr Eastman as the buyer was alone enough to give the jury a reasonable doubt, he said.
He said prosecutors had accused the dead gun seller Louis Klarenbeek of lying to detectives and to the coroner, and that because both he and his wife Joanna were now dead the defence could not test their evidence.
He said the man could not respond to the attacks on his credit.
The silk said the jury would see that the evidence of his wife Mrs Klarenbeek was "riddled with problems".
He said this was a "dangerously weak foundation to base a conviction for murder".
Mr Georgiou said there were good reasons to reject the Crown's allegation Mr Klarenbeek was lying, including that he retrieved spent cartridges that later meant police could identify the murder weapon.
He questioned why if the man was too scared to identify the buyer from a police photo board he would help police in that way.
Mr Georgiou warned the jury they would have to be satisfied beyond a reasonable doubt before returning a verdict of guilty.
Even if they thought Mr Eastman was probably guilty, he said, it was their duty to acquit him.
Earlier on Thursday, prosecutors told the jury the Crown case against Mr Eastman was overwhelming.
On the eighth and final day of prosecutor Murugan Thangaraj SC's address to the jury, he urged the men and women to look at the case as a whole.
He said Mr Eastman had a powerful motive to murder the police chief.
The prosecutor told the jury there was no rational or reasonable alternative to Mr Eastman killing Mr Winchester.
The mafia link had been investigated immediately and exhaustively by police after the murder, he said.
"The Crown has proven the guilt of Mr Eastman beyond reasonable doubt," he said.
Mr Thangaraj had also turned to what the Crown said were confessions made by Mr Eastman alone and in the privacy of his own flat, and captured by police bugs.
"One admission to murder is powerful," he said, adding that there was more than one.
A forensic transcription expert Professor John French was called by the Crown during the trial and he prepared transcripts of the indistinct audio recordings to assist the jury.
One phrase Professor French transcribed was "he was the first man, he was the first man I ever killed."
Another part of the transcript was, "Shot. But why did he/they/I do it ..." and "... had to come back again the next night to (kill the) ... bugger" and "I had to kill him sitting down" and "then (all of a sudden, you're dead)".
Mr Thangaraj said Mr Eastman was confessing to the murder and confessing to going to Mr Winchester's home on January 9, but not shooting the police chief until he returned the next night.
He said the court knew Mr Winchester had been shot and that he had been shot while sitting down.
The trial continues.