Mark,
This could go either way - it all depends on the relative square footages of the different space types. Is it primarily office with a little of the others types, you may be eligible for Energy Star and would need to perform the benchmarking via that tool. If the labs and classrooms comprise a good chunk of the space (more than 10%), than you're definitely looking at a Case 2 scenario.
The way to know for sure is to go ahead and enter the space types into the Energy Star Portfolio Manager tool, and based on the areas in the different categories, the tool will tell you if you are eligible for a rating or not. If not, then it's case 2 for you.
Good luck.