This seems to be dressed up as an article to make it seem like they were just about to file, and then something happened and they decided against it.

Except knowing how the DOJ does antitrust investigations, what happened here is completely normal.

They spent a large amount of time talking with a lot of people.
They decided they either couldn't or didn't want to try to make a case (i'll get more to the "didn't want to"). They dropped it.

The article points out it's notoriously hard to get data on prices pressure, etc (which i'm sure the DOJ did).
"For example, one sign of an uncompetitive industry is the ability to raise prices at will, unimpeded by price pressure from rivals. It's impossible to say, without more information, if the GMO giants have done that—but prices have risen briskly over the past decade. "

Despite the fact that they have no actual data, and admit it's hard to say whether anything happened, they then continue to dress it up in the cloak that because some institute somewhere thought this should have happened, that when it didn't it's all a big conspiracy by "Big Seed".

They continue to go on to point out why the market is not competitive.

The market not being competitive is not the same as having a cognizable antitrust injury that the DOJ can sue over. The DOJ can't sue just because the market is shitty and overpriced. They could sue if Monsanto is preventing new entrants into the market in order to keep it shitty and overpriced, for example. Other than that, the antitrust division as a whole, also doesn't sue people for political reasons.

I've met a lot of the folks in the antitrust division. Even though they are often on the other side of the table from me, these are people who honestly care about doing their job, and the idea that they wouldn't sue if they thought there was a violation and they could make a case is pretty crazy to me. If they felt they had a case, and couldn't get the result they wanted from Monsanto, they would have sued. As a side note, the article doesn't even consider the possibility that the the real result was "DOJ warned Monsanto that if they don't cut out X or Y, they will reopen and sue in the future" or "DOJ came to agreement with Monsanto about X and Y". This is common, and these things tend to leak out over time, but you wouldn't know immediately (any official MOU would have ended up in an SEC filing, but informal ones, ...)

In marginal cases, they make judgement calls, and do try to avoid setting back their enforcement efforts by years by losing (which is the only real case of "didn't want to"). The DOJ settles or issues "memorandum of understanding" in a lot more cases than they sue over, and every time they lose a lawsuit, they may lose some ability to get some good result without suing.

To be clear: I actually hate Monsanto, and think they have set back the world in a lot of ways (particularly in the patent realm). But antitrust violations are a class of behaviors, and the article doesn't point out any actual behavior that falls into it, it just points out (rightfully) how sucky the seed market is for farmers, and then tries to make it seem like the fact that the DOJ probably felt it couldn't have won a case is somehow a conspiracy.