This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
There's more to Karen than at first glance
Danny keeps saying he won't tell anyone why he murdered his aunt. What if Karen pushed Danny to do it at the age of 11 so she could effectively escape the legal consequences of counselling to murder? She's proven to be pretty calculating and willing to jump in with both legal feet at the slightest sign of official notice of Danny in any way.
Jossed with respect to Karen's complicity, but confirmed in that there's hints she's had affairs in the past which may have aftereffects in the present day.
He killed Regina to get the necklace back, and is hoping the fact that he's the most unobvious killer will throw suspicion off of him.
Could be, though that really wouldn't be much of a plan. He'd be kidding himself if he thought suspicion wouldn't fall on the guy who'd already done a stint behind bars for murder.
That said, it's almost too easy to suspect the kid who just got out of jail. A police officer might decide that this would make him unlikely to reoffend, in a kind of aversion of the usual "the obvious guy did it" trope.
The whole "it's never the most obvious suspect" thing never applies in real life investigations. If he's proven to be capable of murder, people will suspect him more. That said, murderers tend to have lower rates of committing the same act again after leaving prison, but since he was so young when he did it, it's hard to say how he'd be viewed by the cops.
Jo murdered Regina
She had 2 motives - Regina had already stolen her former best friend, Lacey and now she wanted to steal her other best friend and sleep with him! This is how she did it:
She pretended to be drunker than she actually was and to sleep it off at home. But as soon as her parents left her room, she doubled back to Regina's house and killed her.
She sent the text messages to Danny to get him to Regina's house or at least implicate him in her murder, and stole Regina's necklace which she recognized that Aunt Tara also wore. Now that Danny is a suspect, she can now "save" him and both of them are getting even closer.
The next morning when she comes over to Danny's house to visit, she drops the necklace somewhere she knows he'll see it. Also notice that for someone who went to bed drunk as a post, she woke up with no sign of a hangover whatsoever!
That's... eerily plausible.
Lacey murdered Regina
For whatever reason, she decided that she wanted Regina dead and a convicted murderer moving to town provided the perfect opportunity. So she borrowed Regina's phone and used it to send those text messages to Danny, including the one about his aunt. This gave him the perfect motive for murder.
Could she be in two places at once? Because that's how it would have to work for her to send texts to Danny without him knowing it was her.
Not if she just left. Imagine this scenario: She tells Danny she's leaving to, say, go get groceries. Instead of going to the grocery store, she goes to Regina's house. On her way there, she sends Danny those texts. Once she arrives, she surprises Regina and murders her. Once she's finished with the murder, she stops and the grocery store to do the shopping she claimed she was doing. She comes home a while later with a bag of groceries and a receipt, giving Danny no reason to suspect that she went anywhere other than where she said she was going.
Problem is, Danny was physically in the same room as Lacey. But that can still be explained - Regina legitimately sent the texts, and then coyly tried the "I know why you killed her" one-liner. Lacey sneaks out early while Danny's still asleep and kills Regina, which conforms to the "approximately 6:30 AM" time of death cited in the episode,
So she pretended to wake up the next morning, clutching the bag of chips to confuse who exactly? The audience?
It's said that his father disappeared after drinking heavily on a yacht. He might have faked his death in order to abandon his wife and son, especially since at the end of the episode Karen said that they're no longer living at their normal standard of living.
This could make even more sense if he had debts that could only be extinguished if a life insurance policy kicked in due to apparently accidental death.
Even more plausible as of the latest episode "Three for the Road".
Perhaps the members of one lodge wear the necklaces, and Danny was "programmed" into the other lodge (probably by his mother) so he would unconsciously kill Tara. How can he explain himself if even he doesn't even know why he killed his aunt?
Danny didn't commit murder at all
Danny's father was having an affair with Jo's mother. This went on until Danny's aunt found out about it and his father killed her, accidently killing her in front of Danny as a kid. Knowing that he would go to jail for life, whereas Danny would go to Juvie for a few years, he let his son take the blame for killing her. This is why he drunk himself blind since he went to prison and eventually died. Jo's mother even coldly mentions how absent her husband was and is now.
Given Danny's latest revelations, this is even more likely. He could have taken the blame, and CSI episodes notwithstanding, a small town is not going to have a fully-staffed instant evidence sifting service in which "the epithelials after being run through Trace and DNA" will instantly vindicate Danny and convict Vikram. Far more likely that Vikram set Danny up with or without Danny's knowledge, and then let his kid take the fall. Danny, in turn, wants to keep his dad's secret, and refuses to say why he "killed" Tara.
Taking this even further, Danny keeps talking about how he's protecting Jo. Not Lacey, but Jo, what if they're actually half brother and sister? What if Danny did kill Tara because he found out Jo was his sister and wants her protected and safe and both of their families not destroyed. It would destroy Jo to know her parents aren't the happy couple she thinks they are and Jo's mother knows something, she is way too cool and sad and reserved. There's just something about her. Even though, he likes Lacey, he says Jo is the most important person in the world to him. What if that's the reason he did what he did and someone still found out?
Confirmed! "Dead Men Tell Big Tales" shows that Vikram killed his sister, and made Danny take the blame for it.
Mayor Rollins killed Regina
Think about this: Whoever was paying off Regina obviously had access to a fair amount of money. (Enough to make regular payments.) And paying someone hush money is the kind of thing that a Sleazy Politician would do. He didn't want her talking about the reason Danny killed his aunt. (Perhaps it would mean some kind of scandal for him.) When he discovered the text she sent Danny, he became afraid that she was going to talk and killed her. Also, getting Danny blamed gives him the added bonus of getting someone he sees as an undesirable out of his neighborhood.
So maybe Vikram really is dead, but the mayor's been using the apartment in Connecticut as some kind of a dead drop, only Regina found out and threatened to tell all.
Given that the mayor has commissioned a private detective who has been basically told to throw enough mud at Danny and make something stick, it seems the mayor does have something to hide. Remember those missing building permits?
This part is confirmed. Chief Masterson finds articles of incorporation for Marna, which meant he was connected with Vikram and Gloria. So the mayor is at least guilty of various monetary offences - probably operating a business under false pretenses, fraud statutes relating to misappropriation of corporate funds, and any conflict of interest legislation that affects him as well.
Awfully convenient that the "murder weapon" gets found after the private detective engaged by the mayor, who we the audience know has been in contact with Regina, insists on combing the lake one more time. Danny presumably handled wrenches at his house. Karen doesn't seem the type to be overly concerned with auto mechanics, so the tools probably just sat intact in the time since Vikram "died". All it would take is for our detective with an agenda to wear gloves, bash Regina over the head, hide the weapon, and then be conveniently available when the mayor needs to pin the whole thing on Danny to make it go away. Legally, even if he didn't kill her, ordering someone else to kill her is equivalent in severity and will get the same sentence.
Vikram Desai was the one who murdered Danny's aunt and Regina found out about it.
Ties in with the above WMG. Danny took the blame to protect Vikram and went to prison. Regina discovered that and was going to go public, but Mayor Rollins didn't want it to get out that an innocent kid had been tried, convicted, and imprisoned on his watch. Fearing for his political future, he bribed Regina to keep her mouth shut. When she texted Danny that she knew the truth, Mayor Rollins killed her to make sure she never talked. This would make a neat way of tying together both killings into one murder case.
And Karen "confessing" is her way of taking the heat off Danny without knowing who the true murderer is.
Seems to be confirmed. Karen retracts her confession after the chief makes it clear he doesn't believe her story hangs together, and he discovers plausible evidence someone who is not Karen or Danny could have killed Regina.
Confirmed, except that Regina may not have known Vikram killed Danny's aunt. She did know that Vikram and Gloria were having an affair, though.
Vikram and the Insurance Policy
Vikram changed the beneficiary of his insurance policy after realizing Danny could still blow the lid off everything, so he effectively set up a $10 million payoff for Danny keeping his mouth shut all those years in juvenile prison. It has the side effect, not necessarily intentional, of forcing Danny to keep quiet because in the event of Vikram's actual death, it would appear that Danny murdered his father for financial gain.
Tess's as yet unknown daughter
The girl is almost certain to be near Jo's age, and could be almost anyone at Green Grove's high school, possibly just a grade or two above. Now that she's been mentioned, she will have to be relevant to the plot in some way.