Idea 1- Games...
As soon as someone said it and mentioned 'Tekken', my brain fired out a few mental pictures. Using the structure of the Eukaryotic and Prokaryotic cells as the 'Bioscientific Scenario' and with having two cell types, its very easy to turn it into a fight between the two. Both have completely different characteristics and the point in the organelles within each cell is that they have a different function that help the cell to work properly.
In thinking through this idea I toyed with which type of layout such a fight could have. Things could go back in time to something like Pokemon on the old Gameboys, but with a little more animation in the characters as they deal and take attacks. The speech bubbles could easily be used to explain what is going on and also each organelles function.
Or maybe bring things further forward and go for a full arena with everything in profile and full colour like Tekken. There could be a commentator voice over explaining the organelle being used in certain situations and so forth. High speed combat might prove a challenge however.
Another layout could be a little more like a turn based RPG (Role Playing Game) much like Final Fantasy. This would allow enough time for a viewer to survey the situation, read all of the information on screen which could contain the details of each organelle, its functions etc. And when an action is 'selected' a short 3D cinematic could be used to illustrate the functions and so forth.
A similar little corner of menu options can be seen in the Kingdom Hearts games, it also possesses short cinematic sequences at various points during gameplay and fights. This menu system is layered over action sequences and not turn based like Final Fantasy. The speed of such a format might prove difficult to emulate.
Last of all an old favourite would be Mario and the Super Smash Bro.s. This platform game layout with some fairly quick action sequences could also work, however communicating the organelles and their functions would have to be done creatively and clearly.
Well thats the game side of things ticking over in my head. Now to see if I can make this work and communicate what is necessary. Let me know what you think and which kind of style you think might work best.