Peter Haynes said he had the "paradoxical mandate" of representing Kony's interests without having any way of receiving his client's instructions.
The fugitive warlord faces 39 counts of war crimes and crimes against humanity, including murder, rape, torture, enslavement and sexual slavery, allegedly committed between July 2002 and December 2005 in northern Uganda.
The three-day hearing at the ICC in The Hague is the first-ever to be held without the suspect present. Kony has not been seen in public since 2006.
It is not a trial but a so-called "confirmation of charges" hearing, where a three-judge panel decides whether the prosecution's allegations are strong enough to proceed to trial.
But in Kony's case, this is a moot point, as the ICC does not allow a full trial to take place in absentia.
Given that Kony cannot challenge the evidence presented against him, Haynes argued the court should "draw a line in the sand" and order a "conditional stay of proceedings".
He took aim at the prosecution's case that confirming charges against Kony would expedite proceedings if he were ever to be found and arrested.
"Seriously? Who does the deputy prosecutor think will arrest Joseph Kony? And where does he think he might be arrested?" he asked.
"In Uganda? By the Ugandan authorities? Well, if that happens, he ain't coming here."
Haynes noted that the high-profile case came at a sensitive time for the ICC.
The United States has slapped sanctions on the court, after judges issued arrest warrants against Israel Prime Minister Benjamin Netanyahu, a US ally.
"Looking at the bigger picture, compromising the rights of suspects through issuing confirmation of charges decisions without any participation of those suspects should not be the future of ICC proceedings," said Haynes.
"Doing so would only give fuel to the fire of its detractors, who wish to portray this institution as illegitimate," he added.
He said the best way to safeguard the court's legitimacy would be for judges to "impose a conditional stay of proceedings at the end of this hearing which can be lifted if Joseph Kony ever appears".
- 'Elephant in the room' -
In response, the prosecution said that freezing the case was "entirely unnecessary" and "completely out of the question."
Ordering such a halt to proceedings would frustrate victims' pursuit of justice, the prosecution said.
A lawyer for the victims, Francisco Cox, said that those who suffered from Kony's alleged crimes want the ICC to recognise them formally.
He said that the argument advanced by Haynes was "creative... but without legal basis."
"They want justice, they want you to confirm these charges," he said, referring to the victims he represents.
"By sanctioning these crimes, you are trying at least to affirm a guarantee of non-repetition and to end impunity to such crimes," said Cox.
Haynes dismissed these arguments in his closing statement.
"The elephant in the room is that this has to stop somewhere. Without an accused, this case is at a dead end," he concluded.
The judges are expected to deliver these ruling on whether or not to confirm the charges within 60 days.
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