This morning I finished the robot animation and rendered the U.F.O animation from Maya.
The robot
The U.F.O
Here's the final edit with both the 2D robot animation and the 3D U.F.O animation composited together
To composite these together, I rendered both the robot and the U.F.O as TIFF sequences, in After Effects and Maya respectively, and then imported them in the timeline together in a separate composition in After Effects.