Thompson was part of a large unit commanded by John Stafford, that was attempting to drive the invading Pandoran soldiers out of New Malaga, during the invasion of Mythos in late 2617. She lost her fiancée when the unit was ambushed. The unit was fragmented and eventually reduced from its initial twenty-one members, to just four. Thompson survived along with John Stafford, Sebastian Smith and Kent Milligan.

Later, she fought alongside Chaz Koonan and Estelle de Winter during the battle of Hunter's Square, helping to drive the enemy away. She later went on to explain to Estelle and Chaz about how the soldiers they were fighting were all infected with nanomachines.

Thompson remained in the CMI during the Pandoran's campaign, becoming involved in a number of offensive and defensive ground operations.

In December 2624, she went with Elliott Parks' fleet to the core Mitikas systems, in search of Jason Zackaria. When the Beta and Gamma teams were taken out while descending to Capitis Duname, Gareth Twineham made her the squad leader of the new Hotel team. She lead her group (which included Christopher Weathers) to the Shard, in search of Zackaria's shuttle. The team was ambushed there, but only Weathers was injured during the battle. Later, Thompson reported to Chaz that the detachment of Pandoran soldiers that had attacked them had abruptly turned around and run away, without any provocation (and without being magged).

Thompson sent Weathers back to Griffin, and returned to Sol, herself, when Parks' retreated back to Helios.