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It is 3D, locked in x-z axis (or locked in 2D basically). The citoplasm may be a calculated 2D model, and the BG uses parallax scolling. Organelles are 3D though.
The model does have a mesh file. But it’s simply a really flat line with a pointy end. The movement is done by the .skeleton file (testing with Clickteam revealed this, I could be wrong). Check game files. I know you can find it there.
Also, the shadow is on the model’s texture. There isnt actually any light source I think.
Not a modeller. I don’t know how the models are converted. I think if you join the team they show you but otherwise, I don’t know much more. Ask @hhyyrylainen, he probably knows. For now make the model. Good luck!
My only guess is to export the model with the same format as the rest (I think it was .mesh) and the bones part (joints) as a .skeleton file. I’d recommend you first check the mesh so you can do the scaling properly.
I haven’t fully figured out the exporting yet. But you need to use blender2ogre (here’s a fork I’m going to fix: https://github.com/Revolutionary-Games/blender2ogre) to export the model as model.mesh.xml and then you need to use the OgreMeshTool (thrive installation builds this but doesn’t put it anywhere, so you need to use it from the ogre/build/bin folder) and then run that with the option
-v2 on the .mesh.xml file to convert it. This should create a binary file mode.mesh that is the right mesh version for Ogre 2.1.