Her name was Sarah. She was not affiliated with anyone and appears to have been acting on her own. Bear in mind that the story of the break-up of the Unity was written before SMAX was envisioned.
EDIT:
http://www.firaxis.com/smac/assets/journey.txt
Sarah Jaydo. (The name is at the very bottom of the link.) The extract below is Episode 35, part 3.
"Release the landing pods." The voice was calm, resonant, and very youthful. Garland couldn't tell if the speaker was male or female.
"I already have. The pods are jammed. It's a mechanical failure."
"Oh?" the figure paused, processing this. "Then there isn't much time."
"We have to get to the center of the ship, to the nexus," Garland said urgently. "I know the..."
"Quiet!" came the sharp retort.
A chill washed down Garland's spine. She doesn't care.
The figure stepped forward and Garland could now see the face. It was a young woman, her face pale and very smooth and clean, but bland. Her eyes seemed dull, lifeless. "Turn around and walk down the tunnel."
Garland shook his head. "I don't think anyone can get down here in time, don't you see? We have to..." A shot cracked the air, a one-off from the shredder pistol, deforming the floor by Garland's left foot. He began to sweat...she was using compacted slugs, and this tunnel was not immune to a breach.
"Turn and move," she said.
Garland turned and began walking down the tunnel. The woman continued speaking. "They sent us into the sky on a hope, a hope based on vanity and self delusion."
He turned back to look at her. "We have almost made it, don't you see?"
She laughed, and the laugh's harshness unsettled him. "I see a square-jawed parody of a Captain, picked for press tours and photo shoots and net views. You are a token, unfit to lead. You were never meant to do anything."
"You're wrong," he said, shaking his head.
"The people that built this ship never really cared if we made it. We are a violent people from a violent world, put into this metal cage to create the illusion of hope for a dying planet. If they really thought the Unity would make it, they would be on this ship themselves."
A chill ran down Garland's spine.
She continued. "Better men and women than you were passed over, believe me. And look at you now...your leadership stolen from under you by others with vision and the will to survive. Now open that hatch."
Garland stopped in front of the hatch, his hands shaking. They were deep in the center of the ship, crossing narrow maintenance ducts that soon would tear away into space.
He pushed the hatch open stud using a sequence that would cause the hatch to close again after five seconds. The hatch opened and a bright, brilliant light washed over him. He put one hand in front of his eyes, blinded.
One second...
"Hands up! Step forward," she barked at him. He lifted his hand again and opened his eyes slowly. He found himself looking into an exterior observation shaft, circled in glass, and outside those panels he could see...
Planet, huge and radiant, a brilliant eye filling the void of space, a living jewel bathed in the light of the Centauri suns.
Three seconds, four...
"Step forward, Captain," she said, "and look at what you lost."
Five seconds!
He dove forward, into the chamber. He heard her yell and saw her lunge, saw the shredder pistol swivel...
Why isn't the hatch closing?
He felt a sharp pain in his throat, and then a wave of ice and fire ran down his torso and up into his face. I'm hit!
The hatch hissed closed, locking her away from him, but he knew she'd have it opened again in seconds. He looked around frantically, saw blood, his blood, on the glass panels, saw a maintenance locker...
The hatch began to open. He threw open the locker and grabbed a closed extensor pole with a gripping vice on the end. Where is the activation stud?
The hatch opened and she came through, her face twisted with rage. He tried to hit her with the handle of the extensor pole and felt it strike her shoulder, than she fired again and he felt himself thrown to one knee.
She stood above him, looking down, death poised to strike. He turned the pole toward her and his thumb found the Activate switch.
The pole lanced open. The kickback rocked through him as the vice struck her beneath the chin, lifted her up and smashed her back into the edge of the hatch. He felt the pole move in his hand as she twisted towards him, her eyes hollow and empty, the vice caught in her throat.
Her body twitched twice and then stopped. Captain Garland looked at her, staring at the shredder pistol in her hand. Was she sent for me? Has it come to this?
He turned to look at Planet again. It was beautiful, so alive, so pure.
He sank into darkness.
