It is alleged that you, and those still at large…

So began each of the 65 charges, read by the presiding judge, in the case against former LRA commander Thomas Kwoyelo.

These charges took over three hours to detail in a stifling Gulu courtroom.

The trial came three years after the formation of Uganda’s War Crimes Division.

The charges detailed crimes Kwoyelo is said to have committed from 1994 to 2005.

They ranged from organizing attacks on civilians, to looting, to abducting children, to the wanton destruction of homes and livestock.

To each count Kwoyelo, wearing a pale green shirt and hair brushed back, shook his head with one emphatic movement.

“Not guilty,” said the court translator each time – not that the movement needed translation.

Kwoyelo stood defiant for the proceedings, his lip curled as if in a permanent pout.

But the most interesting thing about the case was not the meticulous listing of his alleged crimes, but the fact that Kwoyelo has yet to hear back from the Amnesty Commission despite filing an application from prison in January 2010.

The 2000 Amnesty Act states that any person formerly affiliated with the LRA will be pardoned if they abandon and renounce acts of war and/or rebellion against the Ugandan government.

The Act has many critics, like Human Rights Watch, who believe that the legislation effectively gives perpetrators the green-light to kill knowing that they’ll be forgiven down the line.

Furthermore, the Act is vague on who is covered and excluded.

You can understand that former abductees, children who had no choice but to loot and kill lest they themselves be killed, but former commanders?

In fact, this was another argument by Kwoyelo’s defence team.

Former commanders Kenneth Banya and Opio Makasi, actually higher in rank than Kwoyelo, were granted amnesty.

Why then is Kwoyelo, a former abductee himself, being prosecuted?

The cynical amongst us would argue that the three-year old court, with no cases to its name, is striving to justify its existence.

A kangaroo court? Possibly.

Kwoyelo’s family stood outside the Gulu courtroom after the case, united.

He’s innocent, they all said.

That’s certainly yet to be seen in the next few months as over 90 witnesses will be testifying.

But the Amnesty Commission’s delay in a response don’t bode well for the former commander.

The trial hearing was postponed until August 15.