My main theory at the moment is Dot has a got a friend 'in high places', possibly a politician/celebrity/big-businessman, who was an abuser at Sandsview. This friend, or maybe multiple friends, is keen to avoid being caught/killed, so is bribing Dot a lot of money to spanner the any investigation, or as in the case of Danny, vigilantism, against the list of abusers. Slightly more radical extension to that theory is that Dot only joined the force in the first place or certainly got into his position within it purely in order to further this particular agenda - almost certainly helped by the 'friend(s)'.
He's a stooge for the criminal gang of which Tommy Hunter was ringleader, and was groomed from a young age to infiltrate the police so they had someone on the inside - he revealed this to Morton in their conversation in the car park (I actually thought he was going to kill Morton - and he may yet come to regret not doing so). The paedo activities were all part of what the gang got up to. It will probably turn out that he was himself abused.
Going back to series one, the 'Caddy' nickname was explained by a flashback to him as a kid literally being a caddy for Tommy Hunter. It was also made clear that Dot was involved in the conspiracy to frame Tony Gates for the murder of Jackie Laverty.
Going back to series two, it was revealed that Hunter was procuring young girls for clients in high places, including DCC Mike Dryden, which Hunter then used to blackmail him.
Ultimately, Dot was behind the murder of Hunter, but we don't yet know why. Akers told Lindsay Denton that it was because Hunter was getting out of hand but Dot must have had some other motive - either orders from above (this would imply Hunter wasn't actually the ringleader and was working for someone else - maybe a corrupt senior police officer or politician), or because he wanted to take over Hunter's gang himself.
He had Danny killed probably by blackmailing either Hari or Rod to do it, and then killed Rod, not really sure yet why - possibly to fit Hari up for it to get him out of the way?
Yes, that's pretty much what it amounts to. We don't yet know what hold he has over Hari but clearly there's more to it than we are so far aware.
What I don't quite get yet though that I think will become relevant, is what is the link between Tommy Hunter and Ronan Murphy - and what is Murphy's involvement in Hunter's death... ?
Murphy was providing Hunter's clients with access to the kids in Sandsview.
Also relevant is Dot appeared to be really dismayed/worried at Denton's acquittal, and I'm not sure why that is either.
Again, going back to the last series, because she knows too much. Dot was behind her being framed for the conspiracy to murder Hunter. The only reason he let her survive the ambush on Hunter is because a) she had no knowledge of 'The Caddy', and b) he needed someone to make a scapegoat to deflect attention from himself.
Akers and Cole were bumped off because they couldn't be trusted to keep quiet (both worked with Dot but didn't know he was the Caddy, but they might have been able to give away enough info about him for him to be in danger of being caught). We don't know what became of Prasad after the end of series two, but presumably he is still alive and may yet make a reappearance. Dryden too, and some of the other characters from series one.
I think Denton and Arnott will become allies and unravel the whole business.