Earlier:
Update 4:00 a.m: There are now unconfirmed reports the guy in the photo above (and the naked guy put in a police car, see below) was an "innocent" and the suspect actually taken into custody has died at a hospital. If this is true, once again, the media has done a dismal job. For three hours, a local TV station in Boston identified the person in the above photo as the suspect taken into custody, made to disrobe and then put in a police car. Over and over the reporters stressed how smart the police were to make him disrobe first. As of this moment, it's unclear whether the person depicted above was the one taken into custody, or whether the person who was taken into custody is alive or dead. So please read the remainder, live-blogged from a local Boston news station, for what it is: a local news report.
The Boston Globe is reporting one of the Boston Marathon bombing suspects is in custody in Watertown. (Headline here.) They are still searching for the second suspect.
Other reports say that there is no confirmation that the events of tonight are related to the bombing.
Every police agency is now in Watertown: Feds, local, tactical units and bomb details. MIT has been declared safe.
Sirens are still screaming at 3:00 a.m. At 2:40 a.m. police confirmed they are looking for a second suspect. There haven't been any more shots for a while.
The FBI released this much clearer photo of the two suspects today. [More...]
Here's a smaller version. Notice the cop right in front of them.
Update: 3:13 a.m.: All the police vehicles and tactical units have just moved out to a different location. The media assumes they got a new location for the second suspect.
To recap: A few hours after the FBI released the grainy photos, there was a disturbance call at M.I.T. An officer investigating the disturbance was shot and killed. There was a carjacking, and the carjacking suspects went to Watertown, where a lot of gunfire was exchanged and explosives could be heard. One suspect was taken into custody. He's alive because there is now video of him being made to take off his clothes and being led naked into the back of a police car. The second suspect is at large.
Despite the Globe's announcement, there has been no official confirmation that tonight's events are related to the bombing on Monday. Nor has it been established that the men in the FBI released photos are responsible for the bombings. They are only suspects.
The FBI only says the situation is ongoing, and they are working to determine what happened tonight.
Update 3:45 am: Headline of the Boston Globe has changed, but still reports one Marathon bombing suspect is in custody and the other is at large.
Update 4:30 am: The Boston Globe changes its headline again, to report the suspect taken into custody is dead.