Indeed it takes some serious hardware to support the AI — we had to keep it within its own module, and while we could link it with the Command Base or one of our ships, our craft have, shall we say, much more primitive systems compared to what the AI generally works with. The pirate transport the AI hacked to get the weapon out may have had some firewalls, but Infinity has a much larger, much more powerful battering ram, so to speak. She’s normally hooked to a Supercarrier or Fortress Base after all, so a humble Battlecruiser or Command Base is going to make her whine for better gear.
As for security clearance the mission was pretty under wraps given the danger the weapon presented and the tools we brought up to secure it. It’s completely understandable anyone outside of ONI/HICOM would be clueless as to what they were actually guarding.