* In 2000, a rule was passed that clinical trials must include their hypotheses (i.e. clinical outcomes) in their initial registration before the trial is conducted.
* From the graph, the number and proportion of clinical trials through NLHBI with positive outcomes (i.e. an improvement in some health condition) is far lower after 2000 than before.
It was previously easy for researchers to conduct a trial, and then find positive trends in the data to form positive outcomes by framing the data from the trial in a different manner, as if the trial were originally intended to test that positive outcome. This is a problem related to A Priori Probability, where you're essentially turning research, which could have been statistically applied to a larger population given some statistical confidence, into deductive reasoning which doesn't necessarily apply beyond the finite sample size [1] (also see @entee's comment and links for better explanation of why this is important).
This article is stating that the graph implies that, because there are fewer positive outcomes after this new rule in 2000 than before, most of the positive outcomes prior to 2000 (which likely lead to new FDA-approved drugs on the market) must have been illegitimate.
I would point out though, that at least from that graph, the last positive outcome shown prior to 2000 was in 1996, so it's not like it obviously continued right up until 2000 and then suddenly stopped. Even when that rule was imposed in 2000 (I'm not necessarily sure how the ruling was phased in), there was a 4-year gap since the last positive outcome before then, and I don't see another 4-year gap prior to that since before around 1979. I'm not saying I disagree with the article (obviously), but just that while the graphic used seems to imply a trend, it seems like more data would be needed to conclusively show that trend.