The doctor told the jury that the allegations were either made up or hallucinations.
In his summing up, Waalkens said hallucinations were possible, referring to research that hallucinations from sedatives can be visual, auditable and tactile.
Waalkens said although Lim's medical practice was "sloppy" he had never acted indecently.
Four alleged victims testified. All are Maori or Pacific Islander and three of the four are non-native English speakers.
The Crown said Lim's intentions when he administered Midazolam were not medical, but sexual.
Prosecutor Steve Manning told the court that each of the men, aged between 18 and 30, attended the clinic to be treated for minor ailments and woke up from the sedation to find their trousers undone, pulled down or removed.
He told the court Lim had lied under oath, and that he had had administered the drug and taken the risk of sexually touching the men because he didn't think he would get caught.
The jury was told they only had to join the dots to find him guilty of the 13 charges. Manning said it wasn't a coincidence that all four patients had testified to having similar experiences at the same practice with the same doctor.
Judge Rea told the jury that before they could find Lim guilty of stupefying any of the patients they had be sure that he administered the drug intending to commit a later indecent assault.
Judge Rea said Lim would be not guilty of stupefying if the jury found he administered the drug and only later decided to indecently assault the patients when he realised the circumstances.