If you want to write fantasy (I'm about 30 pages into a book I've been working on for 10 years), you need to make your magic believable. One way to do this is to research the magical practices of the past and try to understand the thinking behind it.
Take alchemy, for example. Why did alchemists want to make gold? Not for its monetary value, or even for its beauty, although that was relevant. No, the real reason was that they believed that gold was the perfect metal. In mediaeval philosophy, imperfection is manifested as corruption and decay, and gold does not corrode.
The philosopher's stone was thought of as a sort of magical catalyst that would transform things to their most perfect state. Hence the fact that it is also the elixir of life. A perfect human being would be free from the corruption of disease and death.
But it doesn't stop there. The state of perfection is not simply physical, but spiritual and moral. Anyone using the philosopher's stone would have to repent of all his misdeeds.
So, if an archvillain is trying to get hold of the philosopher's stone, the best thing you can do is to give it to him.