Are there any works, canon or otherwise, that deal with the concept of the Founders, or other shapeshifters, being assimilated or otherwise encountering the Borg?
The idea of an assimilated Founder just came to me, and the difficulty of inserting nanoprobes into a non-solid mass interests me. I suspect the answer to this question is negative, but am curious.
Answer
The only reference I've been able to find is in the DS9 novel : Lesser Evil
"“You resisted the assimilation,” Bowers said. “How?”
A third arm grew out of the center of the Founder’s narrow chest and opened its slender, symmetrical, two-thumbed hand. The arm lengthened until the hand was only inches away from Bowers’s face. In the center of its palm, Vaughn saw, was what looked like a black pebble.
“The nanoprobes?” Bowers guessed.
“They were trying to overwhelm me,” she said. “They were quite painful. They kept twisting me inside out. I knew I had to make them stop. So I did the only thing I could think of. I squeezed them together until they stopped.”
“Mr. ch’Thane,” Vaughn said. “Explain, please.”
Shar shook his head. “She’s fine. She really was able to withstand the assimilation.”
“How?” Bowers asked.
Shar continued studying his tricorder. “Borg nanoprobes are designed to assimilate life-forms on a cellular level. But a changeling’s morphogenic matrix has no cellular structure in its natural state. In essence, it was as if the nanoprobes were trying to assimilate a body of water.”
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