Atari Force has strong characters, highly entertaining single issues, some truly incredible art, and a cohesive central narrative. That's more than plenty of comicbook series contain, but the question remains: is it really about anything? Like all good fiction, there are several possible answers to that question, but I'd like to offer what is, in my opinion, the best one. Because the clear unifying theme of this book, the tragic flaw that so many characters share, is single-mindedness. They obsess over things, create grudges and vendettas where none need exist, refuse to acknowledge other points of view, and argue with each other a lot. This book is a warning against these attitudes, even though they're present in as many heroes as villains.
Martin and the Dark Destroyer's mutual obsession with one another is the largest, loudest example. An anti-matter bomb is set off because of it, killing an entire universe and the Dark Destroyer to boot. Martin loses touch with New Earth, and when he finally gets back, it has been overrun by his enemies and tainted to the point that Martin no longer desires to stay there. His relationship with Tempest is irreparably damaged because of how absent he was in the boy's youth, too busy searching for the Destroyer to be a father. And the Destroyer was equally focused on Martin, even adopting his physical form for the sake of an emotional slap in the face. Martin's life, his connection to his child and the planet he helped found, is beaten black and blue by his insane agenda against the Dark Destroyer; the Destroyer's life literally ends. Neither of them really gets what they want, but both suffer immense consequences for their actions. Their conflict is the crux of the overarching story of the book, and its message is clear: obsession is unhealthy, unrewarding, and unsafe.
Tempest can't grow up all the way or fully control his anger because he spends his free time bemoaning the raw deal he got in the parent department. This is his obsession, and it also prevents him from following his father's orders or being emotionally mature enough to stay away from his ex-girlfriend. This is what ends up getting him arrested, and spending all that time in a cell being force-fed drugs.
Senator Jamieson is one of the most despicable characters in the book, primarily because he refuses to let go of his anti-A.T.A.R.I. agenda. Hunter, a far more likable and layered villain, also ends up on the wrong side of history because of his narrow views of right and wrong. He sticks just a tad too closely to the letter of the law, and it keeps him closed off from the reality of what's happening.
Kargg and Blackjak are both decent and honorable men who became bad guys when touched by the influence of the Dark Destroyer's obsession. Presumably all of the Destroyer's minions are in similar situations, displaying the dangers of single-mindedness when it comes from someone in a position of power. The Destroyer and his forces are the universe's greatest evil and biggest threat, all motivated by his relentless drive to exact his revenge against an old foe.
There are less significant, less serious examples, too. Rident and Pakrat are opposite extremes, but they both represent the problem with letting your family define you. Pakrat spends his whole life on the run, and ends up on Atari Force by accident, risking his life against the Destroyer for no reason other than the fact that he's physically there. A similar thing happens to Rident, so hell-bent on bringing his brother to justice that he ends up just as stranded after the anti-matter bomb goes off.
The entire culture of Morphea's home planet is a denouncement of having too narrow a focus. They are an almost mindless hive, forced to suppress all emotions and sense of identity in the name of keeping their queen content. Morphea questions this, and though it makes her an outcast at home, abroad it makes her one of the most heroic members of her team.
Any rewards reaped from this kind of overly-determined thinking are shown as bad: the Destroyer's power, New Earth developing weapons, Hunter getting his arrests, etc. And more often than not, the characters are forced to face harsh truths and learn painful lessons because of their obsessions. It is the theme at the center of this book, its underlying lesson and, I would argue, ultimate goal. The series is, as I said, a warning, showing many different types of obsession with consistently negative results.