According to reports, he was arrested for causing his pregnant wife injury during a domestic violence report.
http://goo.gl/mlrdj7
Supposedly other members of the 49'ers were present, and according to some reports witnessed him hitting her, but did not intervene.
Goodell can hand down suspension in this case, as he did with Ray Rice although Rice was not criminally charged.
According to the new domestic violence rules, the first offense is six games, and the second is a lifetime ban, but there are conditions which can escalate a first offense into a lifetime ban or a longer ban such as the player being involved in an incident of domestic violence before entering the NFL, use of a weapon, or if the woman is pregnant or the act is done in front of a child.
Sources have said Goodell will not suspend a player unless their case is adjudicated. So if they don't take a plea and aren't found guilty, he won't suspend, but he can. There is no rule in place to prevent him from acting without the courts.
Since this was a pregnant woman, and only two days after the new rule passed, it will be interesting to see if Goodell hits McDonald with a lifetime ban, or if he acts without the courts involvement, just to send a message.
The players union has promised to block any suspension in which the player did not have due process first, but technically speaking, they are powerless here, as they gave Goodell the right to enforce the code of conduct policy of the league in the last three CBAs. The length and nature of any suspension for this is entirely his discretion, and the courts would agree with him.
Even player friendly judges like David Doty won't override the league in a case like this.