After nearly two years of conflicting and often suspect testimony, the so-called Sodomy II trial of opposition leader Anwar Ibrahim is scheduled to finish next week in a Kuala Lumpur High Court, with final summations by both sides.

It is a trial that has been condemned internationally by legal scholars and human rights activists as designed to take Anwar out of Malaysia’s political equation.

Political sources in Malaysia have been building several different scenarios. Given the tone of the trial so far, it appears likely that Anwar, the opposition leader of the three-party Pakatan Rakyat, will be convicted despite a vast number of prosecutorial missteps. That would probably make him a martyr in Malaysia because his followers – and many others – believe he is being railroaded into jail on false charges.

Under another scenario, the judge, acting under orders from the government, would declare him not guilty, which would be followed immediately by a prosecutorial appeal, which would keep Anwar embroiled in more months of legal entrapment that diverts time and energy away from leading the three-party Pakatan Rakyat opposition. It would also give the Malaysian judiciary a thin tissue of respectability.

The story began on June 28, 2008 when a then-24-year-old aide, Mohamad Bukhairy Azlan Saiful, made the charge shortly after Anwar had led Pakatan Rakyat coalition to a historic sweep of five Malaysian states, winning 82 parliamentary seats in 2008 national elections and breaking the ruling Barisan Nasional coalition's two-thirds majority hold on parliament. He was arrested at his home on July 16 of that year, by a contingent of 10 carloads of police commandos and was locked up overnight in a Kuala Lumpur jail.

The trial, which began in February 2010, has been marred by what appear to be the introduction of questionable evidence, egregious prosecutorial errors and a long series of prejudicial rulings by High Court Judge Mohamad Zabidin Mohamad Diah. Critics say the proceedings appear certain to once again tarnish Malaysia’s reputation in international circles and play a role in destroying whatever confidence there was in the country’s legal system. The case has been condemned by the Geneva-based Inter-Parliamentary Union, 60 members of the Australian parliament, Amnesty International and Human Rights Watch and prominent leaders from Commonwealth nations including Paul Martin of Canada and others.

From the very beginning, when Saiful sought to get doctors to certify that he had been sodomized, doubts began to surface. Saiful first went to a private hospital, where a doctor found no evidence of penetration and told him to go to a government hospital. At the first government hospital, doctors also told him they had found no evidence of tearing or scarring that would have indicated his anus had been penetrated. He was forced to go to a third government hospital where he finally found a physician willing to say the act had taken place.

In the intervening months, as the trial has droned on, an array of other doubtful factors have made the case look like it was manufactured to rid the Malaysian political scene of one of its most charismatic figures, and that the country’s court system, never regarded as independent since former Prime Minister Mahathir Mohamad fired the Supreme Court in the 1980s, was bending over backwards to do the government’s bidding.

Gordon Trowell, in a report for the Inter-Parliamentary Union, pointed out that the charges had been levied just as Anwar was making a spectacular return to the political scene from a long period in the political wilderness following his first sodomy trial in 1999, when he was jailed for six years on charges that have been universally condemned as rigged.

Mistakes made over DNA samples call into question whether the evidence could survive in a rational court of law. Police officials have testified that Saiful didn’t offer to be tested for DNA samples until 56 hours after the alleged incident, and he said he hadn’t defecated during those two days, which could have corrupted the sample.

Other testimony indicated that the samples taken from Saiful were kept unguarded in a police office for 43 hours without refrigeration before they were turned over to the laboratory for analysis. Chemists testified that as many as 10 different DNA samples had been found in Saiful’s rear, making the whole analysis process suspect.

That any samples could be taken from Anwar is also questionable. Under Malaysian law at the time, suspects could refuse to give DNA samples. However, the Dewan Rakyat, Malaysia’s parliament, passed a law repealing the consent requirement after Anwar’s arrest. In most courts, law cannot be applied retroactively.

Although Anwar refused to give a DNA sample, items issued to him during his overnight stay in jail were analyzed and a sample was found. Zabidin in March handed Anwar a major victory by throwing out the purported DNA evidence because it had been taken without his permission. However, a week later, after the prosecution demanded it, Zabidin reversed himself and said the evidence could after all be entered into the court despite the retroactive nature of the law.

Then there is the series of meetings that Saiful has acknowledged in court, at the home of then-Deputy Prime Minister Najib Tun Razak and his wife, Rosmah Mansor, on June 24, 2008, two days before the alleged sodomy took place and others with Rosmah's close confidant, the former track star Mumtaz Jaafar, as well.

Saiful also acknowledged meeting secretly twice with Rodwan Mohd Yusof, a senior assistant police commissioner, before the alleged offence took place. Rodwan became famous, or infamous, in Anwar's 1998 Sodomy I trial when he illegally removed Anwar's DNA samples from forensic custody and planted them on a mattress allegedly used by Anwar for a homosexual dalliance. To protect the integrity of the prosecution's case, the presiding judge, Augustine Paul, expunged the entire DNA evidence at the time.

There is also the question of entrapment. Saiful testified that on the day in question he had taken lubricant with him to Anwar’s condominium – hardly the act of an innocent aide who had no idea that the then 63-year-old Anwar was about to jump him for unnatural sex. Surveillance cameras filmed the former aide in a lift in the building but Anwar said he was having a meeting with a group of economists at the time Saiful allegedly showed up.

But the fact that Saiful went to the condo with lubricant in his pocket, whether he got in or not, is ample indication that he intended to try to lure the opposition leader into a compromising position. It would be questionable whether he tried to do that on his own, and it would dovetail rather smoothly with his meetings with Najib, Rosmah, and the law enforcement officials who put Anwar in jail in 1999.

Trowell in his report pointed out a flock of other discrepancies. Abdul Gani Patail, the main prosecutor in the 1998 sodomy proceedings that were thoroughly discredited, has been involved in the present case at a time when he was being investigated by the Malaysian Anti-Corruption Agency following allegations of fabricating evidence.

There was an “almost systematic rejection of all defense applications for disclosure of prosecution evidence, which it would need in order to mount the defense,” Trowell wrote.

There was also the fact that Saiful was having a sexual liaison with Farah Azlina Latif, a female member of the prosecution team, which should have further disqualified him as a complaining witness.

The defense and prosecution have both finished presenting evidence and the opposing sides were scheduled to submit their oral summaries on Dec. 8 and 9. However, the summatons have been postponed until next week at the requesti of the defense. After that the judge will probably take a month or so to deliver his decision. If convicted, Anwar is certain to appeal. Whether he will be allowed bail will again remains to be seen. The process will thus probably go on for an indefinite period.

Unfortunately, what the evidence has shown most clearly is not that Anwar was guilty or not guilty of having what the government termed “unnatural consensual sex” with his former aide. It is rather that the trial was skewed so badly in the government’s favor that the opposition leader demonstrably did not get a fair trial.