From the History Commons Groups blog:

Entries have been added to the Complete 9/11 Timeline at History Commons, which, in particular, reveal new details about events from the day of September 11.

Several entries describe how a group of fighter jets from Otis Air National Guard Base in Massachusetts were taking part in a training mission when the terrorist attacks began. Although the pilots of these jets had seen two other fighters taking off from their base in response to the hijacked Flight 11, they were unaware of the reason for the scramble. They therefore continued with their training mission--described as a "mock war scenario"--over the Atlantic Ocean.

The fighters were recalled to Otis Air Base after the base started preparing all of its fighters for takeoff. At least one of the pilots involved in the training mission soon took off again. Along with another pilot, his first task was to intercept a military cargo plane over the Atlantic. The two fighters were subsequently sent to New York, where they helped patrol the airspace over the city. Before returning to their base, they were directed to inspect a supposedly suspicious aircraft that turned out to be just a tanker plane that had been providing them with fuel.

Military personnel were also concerned about a convoy of aircraft approaching America across the Atlantic, which repeatedly failed to respond to radio communications. But when fighters intercepted the convoy, they found it was just some military planes coming back from Europe.

One timeline entry describes how the military contacted a tanker plane from Bangor, Maine, just after 9:00 a.m. and arranged for it to provide fuel to the fighters launched in response to Flight 11, and yet the tanker appears to have inexplicably been unavailable to support those fighters for the next half hour. Another tanker from Bangor was flying off the coast of North Carolina when the attacks began, in order to participate in a training mission.

Thomas McGuinness is revealed to have only been assigned as the co-pilot of Flight 11 on the afternoon before 9/11, pushing from the flight another pilot who'd signed up for the position minutes earlier. Another entry describes how the control tower at Boston's Logan Airport was called about Flight 11 when contact with it was lost; a tower employee immediately wondered if the plane had been hijacked.

And on September 11, a new entry reveals, the US military's elite counterterrorism force was making its final preparations for a forthcoming major exercise based on the scenario of terrorists threatening to attack the US with a chemical, biological, or nuclear weapon.

Source.