1. Continued with the Freedom Fighters:
Given her strong ties to the Freedom Fighters, it's likely she remained a key member of the group. She could have helped rebuild the Knothole Freedom Fighters after Scourge's defeat, perhaps even taking on a leadership role.
2. Returned to Mobius:
It's possible she returned to Mobius, either with the Freedom Fighters or independently, after the events of the Archie Comics. With the threat of Scourge gone, she might have wanted to resume a normal life.
3. A New Adventure:
Fiona could have embarked on new adventures, either with the Freedom Fighters or on her own. Her skills and experience make her a valuable asset, and she may have sought out new challenges.
4. An Open Ending:
The Archie Comics, where Fiona was a prominent character, ended without definitive closure on her story. This leaves the possibility of her continuing to play a role in the Sonic universe, either in future comics or other media.
Conclusion:
Ultimately, Fiona's fate after Scourge's defeat remains open to interpretation. Based on her personality and past actions, it's likely she continued to be an active and important character within the Sonic universe, though the exact details of her story remain unwritten.