One possible plot could be that Alphys, with her scientific knowledge, gets involved with the Bebop crew while they are on a mission related to some strange scientific phenomenon. Maybe she helps them understand and deal with a new type of space - time distortion.
Perhaps Alphys is a scientist on a distant planet in the Cowboy Bebop universe. The Bebop crew hears about her research that could potentially be very valuable. They approach her, but she is hesitant at first. As they get to know each other, they discover that there is a greater threat looming that they need to face together, using Alphys' scientific expertise and the crew's combat and survival skills.