Solution: An Inky Situation
There was only one way a thief could get off the broken fire escape without injuring themselves, and that was if somebody let them in through the window. After we had left, Templar had discovered the manager of the building crouching on the fire escape, with the stolen microscope. He had been fully prepared to call the police on the thief, but then had realized that the manager was actually his old mentor, Bobby Tapputti. Tapputti had stolen the microscope in the hopes that he could develop the synthetic ink that Templar had been working on by himself, but admitted that his former protégée actually had a much better chance of getting the formula correct. After a brief discussion, the two of them decided to act as if they had no idea who had stolen the microscope in the hopes that Cleo and I would leave them alone, and work on the formula together.
After concluding that this wasn't a nefarious plot of any sort, the two of us bade Tapputti and Templar farewell, and headed off to Hungry's in the Dilemma for a well-deserved lunch.