3D output (stereoscopic) is created by the video card, from the polygons that MA3 provides. Since nothing changes within the code, there's no switch in the program to turn it on or off - that's handled entirely by the video card. On my computer, which has an nVidia 9800 card, there's a checkbox in the nVidia control panel to enable/disable 3D.
Or, get some shutter glasses and enjoy the Aquarium in 3D