You were right to quickly eliminate A, B, and C - "lions" (plural) doesn't agree with "its" (singular). However, we can eliminate E for almost the same reason. In E, "its" must refer to "the lion species". So this gives us:

"Even today, the lion species rules the African plains, hunting almost any animal that crosses [the lion species'] path and intimidating all but the most intrepid hunters."

This creates a strange meaning - an animal crosses the path of the entire species? Do they all travel as one massive group? If we instead use D (which we should also note is more concise), we end up with a more logical sentence:

"Even today, the lion rules the African plains, hunting almost any animal that crosses [the lion's] path and intimidating all but the most intrepid hunters."