He's in an orbital space station of sorts at that time, trying to make sure that the power-source for the on-ground MAC cannons stays intact. Master Chief goes to aid him at one point. We might see them.
Edit: actually, just did a bit of research:
The Covenant return and land troops on Reach with the objective of destroying the generators for the Super MAC Cannons, the only things which are stopping the Covenant. At the same time, the UNSC realizes that the Circumference, a Prowler, is still docked at a station orbiting the planet of Reach just before its fall and has not initiated the Cole Protocol. John takes Linda and James to deal with the Circumference, while the rest of the Spartans were sent down to the planet to defend the Orbital MAC generators.
John's team crash-lands their Pelican on the station which the Circumference is docked on, and they move towards the NAV data. However, James' thruster pack for maneuvering in vacuum is hit by a Needler shard and explodes, sending James flying uncontrollably into space. John and Linda proceed to the Circumference, where they find Sergeant Johnson and his Marines, including Jenkins and Bisenti, also fighting to wipe the data. With John's help, the Marines are successful, but tragically Linda is shot by five separate plasma blasts.
[Edited on 07.21.2009 1:37 AM PDT]