Season three is incredibly strong thematically and, as Mac also says,
Let's start with the relationships. The inner relationships of the team had strengthened last season, and this goes further this year. They are a close family now, and socialising beyond work (as the brilliant scene of Danny and Flack's game of pool can show).
But other relationships flourish as well. Mac and Peyton, starting from the beginning of the season. Danny and Lindsay, turbulent throughout. And both are tainted by the past.
Mac had seemingly let go of Claire in the season 1 finale. But acceptance does not mean moving on, and even though we've heard hints of him dating, there was no serious love interest until now. He has a hard time committing, or even letting the relationship become public knowledge. With someone of his history, we can understand it, but Peyton can't, and shouldn't have to. She is living in a shadow of his wife, and at some point, he even calls her by Claire's name.
The past has a hold on us, and we can't ignore it and rush into the new. Mac has to accept his past before he can think of the future. And that's why him and Peyton won't work in the long term, because he's not quite there yet.
Another instance of past intruding on a budding romance, Lindsay and Danny. It seems like they're starting something, and then she withdraws. And again. And Danny gets mixed signals, clearly. Upon being confronted with it, Lindsay admits that she's not ready, she has things to deal with.
Few episodes later, we learn exactly what it is. She has survived and witnessed a terrible crime, death of her friends. It explains why she is prone to questioning the crimes (as in Stealing Home the previous season), it shows her unable to deal with mothers and families, but it also lines her with Mac among the people still held back by their past. Only after she deals with it, faces the killer, and testifies in the case, is she able to pursue the romantic relationship, embrace a possibility of future.
Past keeps intruding in different ways, too. Familial relationships, for example. Mac encounters Claire's son, Reed. He is a tangible, living link to Claire, and therefore, to Mac's past. He also is trying to learn about Claire, to learn about himself (another instance of investigating one's past to be able to face the present and the future). Reed looks for concrete links to his mother, but there's no grave or body, the only way he can learn about her is through Mac.
Stella and Mindy, her 'blood sister'. Past, intruding on present. By the way of a Cold Case's (the show's, yes) detective showing up with blood evidence (it has to be blood, as blood is family, even the created one). He says the cold cases have a tendency to 'stir up the past', and it uncovers some memories for Stella. It also references one more consequence. Few months ago, Stella says, she would have arrested Mindy. But now she knows you don't choose your hell, and you do what you can to survive. Past, influencing you. Consequences. Frankie's death has changed her, cause and effect.
Cause and effect, consequences, are displayed in pretty much every episode. An accident nine months ago, leads to a brain condition, leads to a murder. Telephone number given to a stranger in a bar months ago could compromise the evidence. An adopted child abandoned by his parents, made to disappear, grows up to become an illusionist who can now make other people disappear... cause and effect. Consequences.
Also present in two main arcs of the season: Shane Casey and Truby/Clay Dobson.
Shane Casey acts in a coldly planned vengeance wrecked at those he holds accountable for the death of his brother, who hanged himself in prison. He's not hiding, in fact, he is teaching the CSIs a lesson (watch out for the next season, where this becomes more of a theme), and he wants them to find things out. He uses a website with snapshots and videos of happy childhood, the past perfect.
But the past and consequences also act against him, when Danny discovers the ring that proves his brother's guilt, not innocence.
And the goldmine of the theme of the season, the Detective Truby and Clay Dobson's case(s). Truby is a dirty cop arrested for murder. Flack, who's butting heads with Mac a lot this season, warns Mac about the consequences of the arrest: every criminal Truby ever arrested screaming for mistrial. And guess what, he is absolutely right. In effect, Clay Dobson, a rapist and a murderer Truby had arrested is let out, and kills again.
Consequences, chain of events. But that's not all. Mac is accused of murdering arrested and handcuffed Dobson, and sacrificed by his bosses in a media-fueled trial that is supposed to show the police officers are not above the law (exactly what Mac was proving while arresting Truby).
And maybe it would have blown over, but Mac had not been playing nicely with his superiors throughout the season, disobeying orders and going around them. Cause and effect.
But then, Truby offers a 'trump card never played', evidence from Dobson's first arrest, that shows that he had already tried to kill himself once to avoid prison, an attempt covered up by no one else, but the person behing some of the media heat on Mac, and his trial.
Sometimes the events go even further back. The solution is always in the past, you just have to know where to look for it.
And the show is not yet done, we'll soon get further back, and dig deeper into the past. Just wait.