An expert who had prepared a mannequin test - about when the body would have surfaced in the water under what conditions - was out of the country and an apparently fed-up judge denied motions for a delay.
But on the trial day, the retired colonel marched off to battle with his head held high.
His onetime Army buddy Russell Preston was also on a mission; he was there to tell the jury how Marecek once boasted he'd never be caught.
In his opening arguments, prosecutor Tommy Hicks told the jury that Viparet Marecek was terrified that her husband was going to kill her.
But the defense said that the evidence - the life insurance and letters - could just as easily show that George Maracek was a good family man and that the state's witnesses were confused or lying.
The judge refused to admit testimony about the dismissed rape charges against Preston. With no proof that Preston was a spy, the defense didn't even bring that up.
Nor would the judge give the defense more time to investigate a new claim by Marecek's supporters that a serial killer in Michigan had confessed to this crime.
Somehow the colonel's team remained confident. It turned out the defense saved its best move for last.
Richard Tobin, a National Guardsman visiting Fort Fisher in June 1991, contradicted Dennis Rood and Tom Deleuw. He said he saw Viparet alone at about the time prosecutors said she took her death march with the colonel.
He said he told his superiors at that time and then let it drop - for nine years until the defense found him.
Encouraged by Tobin's testimony and worried that his training in wartime killing might be used against him, Colonel Marecek did not take the stand.
The defense rested after a six-day trial.
It took the jury less than three hours to reach its verdict: guilty of second degree murder. The sentence was 30 years in prison.
Apparently the jury didn't buy the National Guardsman's story.
"There's no good outcome," said the colonel's daughter, Susan Kirk. "He's my dad, and I love him....I wish I could go back and change everything...but I can't."
For Preston, the man George Marecek had called a traitor and a rapist, the verdict was a final vindication.
For the prosecutor who had tried him three times, it was a sweet victory. "He most certainly deserves every bit of those 30 years," said Tommy Hicks.
For Hana Marecek, the outcome was a crushing disappointment. "I don't understand how the people can do this to a man who spent 36 years fighting for his country," she said.
But what mattered in the end was not what George Marecek did for his country but what the jury believed he did to his wife.
"I'd rather die in prison than confess to something I didn't do," George Marecek declared. "I'not going to be free until I find out who killed her."
"It may take a lifetime," he said. "But that's what I'm going to pursue."
Click here to review how the case started.