Is the article you are talking about "What Putin Really Wants" by Julia Ioffe[0]? It was published in January 2018. It doesn't have the USB key story you're talking about though.
[0]: https://www.theatlantic.com/magazine/archive/2018/01/putins-...
[0]: https://www.theatlantic.com/magazine/archive/2018/01/putins-...
And the breach happened in Kabul, NOT the Pentagon.