"Now, I'm sending you some ammunition, some medkits, some grenades, and a change of underpants. Don't forget to wash behind your ears".
GeneSYS has unusual ways of putting things, but once Bob gets used to it, he's forced to admit that maybe that's just the result of being not quite human. And GeneSYS' methods are effective.
GeneSYS is not all-knowing for one reason or another, and can be excused for leading you into traps that it didn't know was there.
Double Subverted: GeneSYS had a second layer of programming placed by the true antagonists that causes it to start giving Bob useless or dangerous instructions once he's into the facility far enough that fighting his way back out is impossible.
GeneSYS constantly tells everyone in the facility —including allies and hostiles— about Bob's embarrassing secrets, whenever possible.
GeneSYS: (hijacking the facility's speakers) "Aaaaand... did you know that Bob browses TV Tropes 8 hours a day?!"
GeneSYS Likes to read its awful Slash Fic featuring Bob and other characters over the facility speakers.
GeneSYS: "Bob, his skin flushed with anticipation, reached for Joe's throbbing-" Bob: "Stop saying words".
Invoked: The bad guys are unpredictable by normal means, so a Confusion Fu AI with the abilities of a Mad Oracle is required. Therefore, GeneSYS is programmed to have a highly unbalanced personality so she can fully predict what the villains are doing. Bob endures GeneSYS's come-ons and passive-aggression for the sake of her occasional bouts of insight.
Exploited: GeneSYS was originally an attempt at making an OS for Ridiculously Human Robots, but the flawed programming lead to her being unbalanced and occasionally nonsensical. However, she also has Mad OraclePsychic Powers due to a mysterious program interaction no-one has been able to isolate, so the military bought her source code and made her into a Mission Control AI.
Defied: Bob smashed his internet connection and decides to take the mission on instinct.
"Okay, here's the three available Mission ControlAIs we have for you. GeneSYS was designed as an experiment to see its charge as an object of affection, but always goes too far. Everyone who uses it has reported being "seriously creeped out, man". CoRE is better for direction, but has an obsession for asphyxiating kittens we've been unable to get rid of. This last one, WALtEr has a vocal glitch that causes it to take on a cockney accent, but is otherwise well-balanced. So that's the one you'll be getting".
"Again? I don't know how these systems keep going sentient and developing stalkerish obsessions for intruders".
"I don't understand these AIs at all. I've bypassed or wrecked at least eight different security measures. I've cause millions of dollars of property damage. I've killed more faceless henchmen than I can count. And all the voice can say is how happy we'll be together?"
Bob is going in blind. With faulty information from a source he has no reason to distrust, he gets ripped apart like a schoolgirl in a bad hentai movie.
The game has a female protagonist, and the stalkerish AI has a male personality, to highlight a double standard: Female stalkers are either amusing or romantic in a weird sort of way. Male stalkers are just creepy.
Reconstructed: The people who programmed GeneSYS knew that a dull droning robot voice would grate on people's nerves all day long, so they programmed it with just the right amount of Deadpan Snarker and Manic Pixie Dream Girl so that the employees would be entertained. GeneSYS likes to tease people who are edgy about computers to get them to loosen up.
Played For Laughs: GeneSYS obviously isn't intended to be taken seriously, and fails hilariously at a) convincing Bob that it's trying to help him and b) slowing him down at all.
"Bob! Listen to me! In order to progress further, you need to flood the kitten containment area with cyanide!" "I have a key. I found it under the safe you specifically told me not to look under. I'm ignoring you now".
Played For Drama:
GeneSYS is a Ridiculously Human Robot, and it and the protagonist have feelings for each other. Which makes strange things happen when the protagonist does something that confuses GeneSYS' programming.