Rogue knew the VI was lying the second she started speaking. She was either working for the enemy or was being forced against her will to. He felt Shepard get much closer to him. Her next words were soothing to him, this was probably due to her being so close.
"Wow she's right next to me" said the organic voice in his head.
"That filthy organic doesn't have feelings for you and you shouldn't care" said the synthetic voice in his head.
"Is she lying?"
"Its quite obvious, relax I got got a back up plan," Rogue whispered back.
Rogue turned to the VI once more speaking in binary again.
"0101010101010101010101010100001010101010101010101 01010101010100001010101010101010101011101010101010 1010101010101010101010101010"(Translation)
"My mission is to bring these useless organics in dead or alive and claim the artifact in the name of the Reapers so I'll ask you again. Where is the Prothean artifact?!?!."