Even though the 49ers organization had been standing by defensive end Ray McDonald and vowing "due process" for domestic violence allegations against him, a new sexual assault investigation that just arose this week. As the Sacramento Bee reports, McDonald is the sole suspect in the sexual assault of a woman who arrived at a San Jose hospital Tuesday morning. Police then went to McDonald's house to serve a search warrant, and it was the third time police had been called there in the last six months.

Just last month the Santa Clara DA's office decided not to file charges against McDonald in the August 31 domestic violence incident involving his pregnant fiancée. In that case, the DA struggled with evidence that the fiancée had hit McDonald, and that she had pulled a gun on him during a previous incident in May.

The woman involved in the current investigation is not McDonald's fiancée, and 49ers general manager Trent Baalke now says, "This is about a pattern... this is just a pattern of decision-making that Ray has demonstrated over the period of time that, once again, it’s no longer going to be tolerated [by the organization]."

Sensitively, the Chronicle writes:

The impact on the [49ers'] defense pales in comparison with the gravity of alleged sexual-assault charges, but the 49ers will miss McDonald’s run-stopping presence in their 3-4 system. Since McDonald became a starter in 2011, he’s missed just three of 62 games and the 49ers ranked no lower than fourth in rushing yards allowed from 2011 to 2013.

They rank eighth this season despite a rash of key injuries, and McDonald had 39 tackles and three sacks in 14 games.

They also got reactions from fellow teammates about the firing of McDonald, who had been with the team since 2007. "It’s tough," says Colin Kaepernick. "He’s a good friend to a lot of people on this team... So, hopefully, it’s just a misunderstanding."