In theory science is limited only by the universe (it will never figure out what happened before the big bang). In practice; the biggest limitation is human limits. You have to be able to question something before you can investigate it, you must also be willing to ask the questions.
One limitation of science, is it's inability to see beyond strict circumstances and tests.
ANSWER: Science is the method of describing nature. What science has thus far failed to do is describe the nature of nature.