For scene 3, I wanted to show the transition between focusing on the veins, and moving into the underwater scene. I copy/pasted the vein and discs from scene 2, and placed them in my underwater scene with the fish and lily pads.
Next, I needed to animate the discs sliding through the vein. I attached the discs to a motion path. I tried attaching multiple discs to one path, but they all bunched up into one shape, or I received errors from Maya, so I duplicated the path and made a few tweaks to each one so it varied slightly.
In the end, I wound up using multiple motion paths and the Hypergraph Editor to tweak how each one animated, so I could get some variation in speed over distance.