Issue #1: How would the ship react to "aliens" (PCs) on board? Assuming it is smart enough to realize it may need their help to survive, I'm thinking it might 'cooperate' at least a bit.
Issue #2: How would the ship communicate with the "aliens"? Would you treat it as just another NPC who doesn't speak the same language?
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Assuming that the AI and the 'aliens' speak the same languages, there are some things to consider:
1) An AI, while possessing a sophisticated stimulus-response decision tree, can not reason beyond its database. The exception would be those neural-net types that can actually learn by induction. Thus, if the AI possessed the equivalent of Steward-8 and nothing else, it would not necessarily be capable of operating a starship, even if its equivalent IQ were 300+ and it had access to the entire ship's library, unless it could both learn and understand the data.
2) An AI may only be able to effectively communicate within the context of topics related to its intended functions. Consider a nerd; he or she may go on for hours about 'Magic: The Gathering' or the musical styles of Enya, but beyond this, their conversational abilities will be full of references to their special interests.
("When will lunch be ready? Who knows? Only time...")
3) Read this article on
Asperger's Syndrome, and apply the concept of a person with 'Highly Functional Autism' to your AI PC/NPC. The key phrases are
"normal intelligence and language development" and
"marked deficiencies in social and communication skills."
4) Communication should not otherwise be a problem, once you figure out what the mode of communication is ...
"Okay, try this: tug your left ear twice, blink, and hop on your right foot ... good ... now that we have life-support running, let's try to get the m-drive on line... take your right hand and grab your... GESUNDHEIT! Well, now we know the missle launchers work..."
5) Also, keep this in mind, especially for AIs running military vessels and high-TEC dictatorship-run worlds:
"Worlds governed by artificial intelligence often learned a hard lesson: Logic Doesn't Care." -- YIN-MAN WEI, "This Present Darkness: A History of the Interregnum", CY 11956 (from the TV series "Andromeda")