Step 1: Rough animation of Twilight in Adobe Animate.
Step 2: Film the live action portion for several hours. I had a friend hit the desk from underneath to make everything shake (shoutout to Lunatic Andrew), and it took a long time to get the set ready. Lots of makeshift light diffusers like milk cartons and spray bottles, and a placeholder piece of paper with tracking markers.
Step 3: Finish the 2D animation in Adobe Animate to match the live-action timing best.
Step 4: Stabilize the shot with using multiple methods in After Effects
Step 5: 3D track the shot in Blender and reconstruct the scene.
Step 6: Trace the 2D animation on to paper (111 frames)
Step 7: Scan the paper animation into the computer and put it together in Premiere.
Step 7.5: I forgot to add my watermark in, so I drew 5 or so blank frames with my watermark and then composited it onto the 2D animation in After Effects and Premiere.
Step 8: Animate the pencil in blender.
Step 9: Render a shadow pass and a pencil pass.
Step 10: Composite the paper onto the original, after some color correction, then composite the pencil and shadow layers from the 3D render.
Step 11: More special effects (explosion, magic, etc.)
Step 12: Lotsa color correction.
Step 13: Record sound effects (the pencil sounds, the wobbling button sounds, the wooshing, and the table shaking sounds were all recorded by me)
Step 14: Rip some sound effects from the show. (I found a version of S4E26 with no music and cut parts out of that, mostly, and then got a bunch of hoofstep sounds from someone else.)
Step 15: Anything I might have forgotten along the way.