D3 would load, the AJAX call to fetch data would complete successfully, even the axes would render, but the data would not plot!. There weren't any exceptions thrown and there weren't any console log statements, so I didn't have any clues to lead me in the right direction. After inspecting the generated HTML elements I realized that D3 was, in fact, generating the coordinates for the SVG, all of the lines, shapes, etc. However, the opacity was set to 0.000001 for all of those elements. So, within the developer tools I slowly set the opacity level to 1 on all of the relevant elements and I could see the chart as it was intended. I was clueless as to why it would set the opacity incorrectly, but I figured I would just counteract that by explicitly setting it to 1 for all of the relevant elements once the chart had rendered. I did so, but then anytime I interacted with the chart and a transition should occur all of the opacity levels were overwritten and the chart looked like crap again.
I was dumbfounded. The chart worked perfectly when we were developing our module outside of this web application, but I could not get it to render correctly within it. After extensive Googling, I eventually found an article/GitHub issue (https://github.com/mbostock/d3/issues/1302) that described my exact problem and the exact solution. D3 relies on the standard Date object within JavaScript (it's now() method specifically), but the web application that I was integrating my charting module into was using Date.js; which overrides the method and breaks the standard. This was causing all of the transitions to fail...silently (no exceptions, no log statements).
Although I knew that there was a conflict of some kind somewhere, I was pretty close to looking into other charting/graphing libraries. It was that or step through D3; which I just didn't have the patience for at the time. Kudos to baversjo for doing that work and identifying the problem. The point of this post is just to direct more attention to the cause of the error/unexpected behavior, shed some light on the situation, and really just prevent me from dealing with this madness again in the future. :)
And for the record, I REALLY wish that D3 just logged the fact that the object returned by Date.now() was not of the expected type. It would have saved me a lot of time.