I personally think they're trying to create APTX4869 to become immortal like Pandora's power. If Snake is part of the Black Organization, it would be why he wants Pandora so bad. Maybe they need Pandora for research. The volley comet is said to come every 10,000 years. Unless that's coming up soon, they probably want to become immortal and can't wait that long. Perhaps it failed, and they realized it killed instead. So, they started testing it on lab rats. It was rare for them to survive though. So, they started using it to kill people. Maybe... The Boss actually WANTED someone to be shrunk so the research could move forward. There's definitely a chance the Boss knows about Conan.