He entered the US illegally, so he can't do Adjustment of Status in the US. (An exception is if he was petitioned by anyone before 2001; in that case he can do Adjustment of Status in the US. Another exception is if there is any immediate member of his family who is an active member of the US military; there is a possible way to do it in that case.) That's why they say he has to leave the country.
If he stayed more than 180 days and then leave the US, he has a 3-year ban; if he stayed more than 1 year and then leaves the US, he has a 10-year ban. If he wants to return before the ban runs out, he needs a waiver. That's probably the "pardon" you're talking about. However, an immigrant visa pardon for this ban can only be based on hardship to his spouse or his parent who is a US citizen or permanent resident. It's not clear from your description who would be the qualifying relative for his waiver.