I am trying to run some d3js on my MVC 6 and was looking at this example https://github.com/DustinEwers/D3-DotNetMVC-Demos/blob/master/D3Demos/Views/TagDemos/BasicBarChart.c
If you just wan't to run that script, simply create a html script tag:
But i really recommend that you bundle and minify your asset files. You can bundle, minify, move (and a lot more) your javascript/css files with the help of taskrunners like Gulp and Grunt.
Information on how to use gulp can be found here: http://rudiv.se/Article/asp-net-5-bundling-with-bower-and-gulp
And then with the help of Shyju post load correct files when you run your development or staging environment.