Battle of Earth
At the start of Halo 2 the In Amber Clad was docked at Cairo station for an awards ceremony that was honoring the Master Chief, Sergeant Johnson, and Jacob Keyes. Since Keyes died on the first Halo, his daughter, In Amber Clad's commanding officer Miranda Keyes accepted the Colonial Cross on his behalf.
A small Covenant fleet quickly showed up to attack the station and the other orbital MAC guns so they could make their way to Earth. After the Malta and Athens were blown up from the inside it was deduced that the Cairo also had a similar explosive on aboard and the Master Chief began his mission to give the Covenant back their bomb. Chief was picked up by the In Amber Clad after the bomb was returned and Keyes decided it was time to take the fight to the service. On the surface the In Amber Clad, acting as a command station, dispatched marines and also treated the injured. When the Covenant assault carrier Solemn Penance initiated a slipspace jump within New Mombasa, the In Amber Clad was given the go-ahead by Lord Hood to pursue.
Delta Halo and High Charity
Upon exiting slipspace Keyes was informed by Cortana that they had arrived at another Halo. Keyes dispatched the Master Chief and a team of ODSTs to the surface to find the Prophet of Regret, while she and Johnson went to the Library to get the index so the Covenant couldn't fire Halo. They fought through the Flood and made it to the index, but were captured by the Arbiter and, in turn, taken from him by Tartarus. Having no need for the frigate the In Amber Clad was left behind.
The Library and surrounding areas were overrun with Flood, eventually boarding the ship. The Gravemind used the In Amber Clad to crash into High Charity so it could spread the Flood to it's huge populace. Cortana told the Chief that if they had to she could detonate In Amber Clad's reactors to destroy High Charity. This never happened as the Chief followed Truth, and High Charity fell to the Flood leaving Cortana in the clutches of the Gravemind.
The ship was not seen again. However, when the Chief returns to High Charity at the end of Halo 3 to rescue Cortana he overloads the reactors in an effort to kill the Gravemind. Along with the Arbiter they escaped in a crashed Pelican before High Charity explodes. It's highly likely the Pelican came from the In Amber Clad.
In Amber Clad's hull classification is FFG-142. 1+4+2=7, a number significant in Halo and other Bungie games.
If one looks closely, at the beginning of Halo 3: ODST you can see the ship following the Solemn Penance into the slipspace portal.