It makes sense if you make some punctuation changes. Semicolons are used to separate two independent clauses, and the clause following the semicolon is a dependent clause. A useful quick rule of thumb for semicolon usage is if the semicolon can be replaced by a comma and a coordinating conjunction (for, and, nor, but, or, yet, so), then the semicolon makes sense in the sentence. Since here it does not make sense to say "...in its place, and the ominous branches of which...", a semicolon is not appropriate.
Also, the "The" in the middle of the sentence should not be capitalized.
So instead, you have:
The once inviting deciduous flora of northern Minnesota had left but a skeleton of its former self in its place, the ominous branches of which stretched across the dimly-lit road, as if they were only mere seconds away from snatching on-coming vehicles from off the ground.
This is correct, if a bit run-on.