Emma was able to evacuate from Theta when it was attacked and overrun by Terry Akers and the Proxies. She and the rest of the crew who escaped all met their deaths before they were able to get into Omicron, due to the quarantine.
Emma and Richard Thabo seem to be the last of the evacuated crew to die. Emma and Richard have a friendly conversation before they both suffocate from lack of oxygen.
In SOMA
Emma's body can be found by Simon Jarrett outside of Omicron. Her blackbox can be mined to discover her fate.
