On Natural Instincts, the story of True Blood starts mid-season 3, after episode 9 ("Everything Is Broken "), while using some storylines from episodes/seasons afterwards.
The Search for Russell
After Eric Northman killed Russell Edgington 's lover, Talbot, Russell struck fear into the nation with his infamous speech on television, ripping out a reporter's spine and fleeing to NYC.And after sharing a kiss with Sookie, Eric was tempted by Pam to use Sookie as leverage. Eric agreed with this - so they both kidnapped her and took her with them to NYC.
The Search for Sookie
Bill sensed Sookie's distress, but finding no one at Fangtasia, he searched Sookie's house. Jason just told Tara that he killed Eggs and wanted to come to Sookie for comfort, but instead he found Bill there. Bill was quick to tell Jason that Sookie was in trouble and that he was going to Fangtasia one more time to see if there was anything he missed. Jason insisted that he help. Hedidn't trust Bill with Sookie, and he also wanted to find his sister.
When they got to Fangtasia, Bill glamoured a human into revealing Eric's (and Sookie's whereabouts) - New York City. She even revealed that they were starting a business venture to expand Fangtasia as a franchise. Both Bill and Jason were willing to go to NYC and rescue Sookie, no matter what. Bill tried to discourage Jason but he was severely focused on protecting Sookie and not screwing it up this time.
First, Bill went to Jessica and told her the situation. Hyott was there as well.
- Jessica: You're what? You're leaving? For how long?
Bill: I am unsure.
- Jessica: But...But you're coming back right?
Bill: Jessica, I cannot determine that right now - I do not know myself.
Jessica: Well you can't just leave! You haven't released me -
Bill: - actually, I have -
Jessica: -Well not officially! And I don't care!
Bill: - Jessica -
Jessica: - I'm coming with you.
Hoyt: [Puts an arm around her] We're coming with you.
Jessica: [Smiles at Hoyt]
Bill: [commanding] I will not allow this. You will only be endangering yourselves and, Jessica, I cannot take care of you.
Hoyt: I'll take care of her, vampire Bill. You have my word - nothing's gonna happen to her. [kisses her forehead]
- Jessica: Bill, please let us come with you. W-we can help you! It's not like we don't wanna find Sookie too!
Bill eventually agreed and allowed them to travel to NYC with him. Hoyt and Jessica moved in together. After a month or so in NYC, Jessica started giving into a few temptations of being a vampire in a large city.
Jason went the police station to tell Andy he was taking a trip (Bill gave specific instructions to Jason not to inform the police) to NYC, explaining that he didn't know how long he'd be gone.
- Andy: Well Jason - I hate to see you go. But I ain't the one to tell nobody what road to take and whatnot. So if this trip 'a yours is somethin' you think will do you some good - best of luck to ya.
Jason: Thanks, Andy.
Andy: Be sure to send a post card or somethin' of the Statue of Liberty. The folks over at Merlotte's would love to see somethin' like that. I always kinda wanted to go site seein' over there my self.
Jason: Sure thing. Hey, uh...can I ask you a favor?
Andy: ...well, depends on what kind of favor you talkin about.
Jason: [leans forward at the desk] You, uh...you think you can put in a good word for me over at the NYPD?
Andy: Jason, what you think I look like? Some national police hub? I don't have any pull over there! I've never been to New York City!
Jason: I know that, Andy! But can't you do...somethin'? I figure while I'm in the city, I might as well take advantage - see what I can get myself into. Think about it Andy. ' Jason Stackhouse - NYPD.'
Andy: Yeah, I'm thinkin about it and I ain't likin it. [sighs] Tell you what - I'll write you a reference letter.
Jason: Thanks, Andy! [reaches over the desk to hug him] I owe you, man.
Eric and Pam had set up residence at a vampire hotel temporarily, until Fangtasia:NYC was finished being built. They still held Sookie as their prisoner - tying her up in chains in their suite.
Jason stayed in a separate hotel from Bill (no way was he even staying in the same building as him - no offense to vampires), but Jason still was Bill's right-hand man when it came to figuring out where Eric was. As it turns out , Bill, Eric, and Sookie were able to incapacitate Russell. Bill and Eric buried him in cement. After all that teamwork, however, Eric revealed to Sookie Bill's true intentions when he first met her. This all caused Sookie to reject both vampires. In the end this didn't matter, because right before Russell was buried he revealed that he had more vampires looking for her in Louisiana. He bragged to them that they were stupid enough to believed he was alone in all of this and they haven't seen the last of him. Both Bill and Eric didn't want to take a chance, so they kept her in Fangtasia against her will.
Jason did everything to get to her but Bill and Eric made this impossible.
- [While Eric and Bill allowed Jason to see Sookie]
Jason: It's okay, Sook. We're gonna get the hell out of this place - take the first plane back to Bon Temps. And if I ever see those fangers again I'll -
Sookie: Don't you say that, Jason. That don't even sound like you. And I don't want you doin anything stupid.
Jason: It wouldn't be the first time. And those vampires keep hurtin you, Sookie. I can't stand for that. Sookie: I've seen just enough killin and revenge for one lifetime, Jason. I don't need you to add to it.
Jason: Alright...well, we'll be out of here as soon as you think its time. Just say the word. They can't keep you in here forever.
Sookie: They won't, I can guarantee that much. [sees a pamplet marked NYPD] What's this, Jason?
- Jason: Oh it's nothin. I was tryin to build up my reputation - besides, I can't pass up a chance to work for the NYPD can I?
Sookie: Any luck?
Jason: Yeah they put me in as an intern.
Sookie: Congratulations, Jason! [pause] You know, staying here doesn't seem so bad. Its busy and loud but...it's kinda excitin'.
Jason: And the girls here-
Jason: Well I can't help natural fact, Sook.
Sookie: Sometimes I feel like I take all the shame for you because you don't have any.
Jason: That's probably true.
After a couple of months, Sookie did make her last straw against the vampires - discovering just how powerful her fairy energy was when she tried to force her way out of captivity. Bill and Eric had no choice to let her go. By that time, most of her friends had followed her there and made a life in NYC....oddly enough. She was content to stay in the city.
A Change For Sam
Sam almost killed a man at his bar and shot Tommy in the leg. Once Tommy healed, he - already having a heated, impulsive temperment - decided he didn't need Sam or his parents, he was fine on his own. So he stole the bar's money and fled - no one knew his whereabouts.
This sent Sam over the edge. He decided he couldn't stay in Bon Temps anymore. He had to get away from it all - just get into his truck and go somewhere far off. After all, he had pushed away everyone he's cared about. Merlotte's was his dream - but it wasn't supposed to be like this and he felt he'd be more harm than good to the place. He briefed Terry about his decision, putting him completely in charge - pretty much giving him the restaurant for a while.
- Terry: Sam...when are you coming back?
- Sam: ...[sighs heavily and looks up at him]'
- Terry: [pained] You're not coming back, are you?
Sam explained to him that he honestly didn't know - he had to figure things out for himself. Terry, of course, vigorously tried to convince Sam he was making a mistake but he didn't budge. After selling his real estate apartments, Sam left.
Before Bon Temps, he had a whole life of thieving and conning (and murdering), something no one in the southern town knew. He needed to reconcile himself with that part of his life, so he decided to face it head on going to one of the places he used to stay (and where he essentially stole as much money as he could) during his old life - NYC.
He began working at a place specializing in Louisania cuisine (The Delta Bar & Grill ) as assistant manager, until the owner died. Sam is now in charge.
A Change for Tara
Then, there's Tara. It had been sometime since Sam left when Jason confessed about Eggs. At that point, Tara didn't know who to trust. She stayed with Lafayette for a while and he took care of her.
- Tara: I don't know anything anymore, Lafayette!
Lafayette: Hooker, just tell me what you mean and stop speakin in code.
Tara: I mean I can't trust nobody. After what that dead fucker Franklin did to me, I look at this town and its like I'm in the mu'fuckin Twilight Zone.
Lafayette: Trust me, this ain't no Twilight Zone, Tara.
Tara: You right. It's worse.
Lafayette: Look, you just need to take a breather.
Tara: Bitch, I ain't tryin' to take no drugs from you right now and I ain't--
Lafayette: -bitch, calm down! This ain't about no drugs. But if you want any -
Tara: [snappy] I don't.
Lafayette: I was about to tell you to take your sorry ass up to the corner store and get your own damn aspirin. Shiiiit. [grins]
Tara: [laughs] You know what? I wish I could just live another life, you know? Be a completely different person.'Lafayette: Listen. Take some time for yourself. Put all them other folks on hold for once and focus on numero uno. And if you need a change, Tara, make that shit happen.
Tara really thought about his words and took them literally. It was time for a change. She cut her hair, got in her car, and took all the money she had to book a one way trip to NYC - away from every single possible thing that could remind her of Bon Temps and subsequently, her old life.
Some weeks later, Lafayette gets a call from Tara while he was with Jesus.
- Lafayette: Hooker, where have you been? You know I've been sittin up here worryin about you, thinkin you done ran off and did something stupid.
'Tara: Well... you could say that.
Lafayette: Bitch, start talkin.
Tara: I'm in New York City.
Lafayette: Run that shit by me again?
Tara: You heard me. I'm in NYC!
Lafayette: Now tell me how and most importantly, why the fuck did you get yo' skinny ass all the way up there?'Tara: Well I took what you said to heart and you were right. I needed a change. A big one.
Lafayette: Bitch, that don't mean high tail yo' ass all the way up north! Tara, from now on, I ain't sayin' shit else to yo' crazy ass.
Lafayette: You think I'm playin with you. Hooker, that is a mistake.
After the conversation was over, Jesus had heard most of it. He voiced an idea to Lafayette: Maybe they should move to NYC themselves. At first Lafayette thought Jesus lost his mind. But he started explaining that he knew that he could learn so much from the wiccan activity in NYC. He'd been saving up to go but never saw the opportunity. Now convinced that Lafayette had 'power,' Jesus felt he could benefit too. After much debating and convincing, Lafayette decided to go with Jesus' plan.
Sam Merlotte & The Delta
Once Same started getting used to running the place, he had an unexpected customer. Tara.
- Tara: Oh my god, Sam Merlotte!
Tara: This is a small world, ain't it? I guess I can never get away from you Bon Temps mu'fuckers, huh?
Sam: [laughs] 'Guess not.
Tara: So what brought you all the way out here?
Sam: Uh...well, I guess I needed a change.
Tara: Well guess what? You're gonna get a lot of shit from me about just up and leavin' like that. [grins] Not that I should be the one preachin' though.
Sam: [laughs a bit] So what made you come all the way to NYC?
Tara: [smiles at him] I guess I needed a change too.
Eventually word spread, and other Bon Temp regulars found The Delta - including Lafayette and Sookie, who continue to work under Sam's management.
Meanwhile, Sam found a shifter group in NYC. There is where he met Luna, and he began developing a relationship with her. She had some baggage - a big one being that the father of her little girl was an unstable wolf pack master named Marcus. But it was then that Tommy found Sam, telling him he's killed their parents. Guily, Tommy shifted into Sam and got himself killed by Marcus. Sam tried to avenge his brother's death but Alcide ended up killing Marcus instead.
As hate crimes against vampires and others started to rise, the shifter pack Luna and Sam were involved in was massacred by a group of unknown hateful hunters, without mercy. Luna was one of the victims but her child, Emma, escaped. Sam took care of her for a while but the mother of Marcus was looking for custody. Alcide, now leader of this pack, pressured Sam to hand her over.
Life in NYC
Once sticking around NYC, she was lured into faeryland. She saw how horrific it was and also discovered that when she spent only about an hour or two in the world, she loses a month or two in the real world. When she came back from Faery land, she had to get used to the changes.
Past Regression Spell & Eric Northman
A strange spell went wrong and affected a certain amount of people - including Eric Northman. He lost his memory but revealed a different side to Sookie never before seen. Both Sookie and Eric got closer during that period - and given the chaos surrounding vampires after the spell wore off - both Eric and Bill did not hesitate to save Sookie on numerous occasions. Still, Sookie chose neither vammpire.
Lafayette began discovering his powers along with Jesus. Periodically, he would become possessed by ghosts. One day a malevolent ghost used his body and killed Jesus. Even after this whole incident, some magic, demonic power is making him do crazy and dangerous things - and it's scaring him.
After Debbie witnessed Alcide kill Marcus, she went on a rage - came to Sookie's house and took a shot at her. Tara was shot instead, and immediately Sookie shot Debbie. Pam was around looking for Eric, but ended up turning Tara into a vampire with convincing from Sookie and Lafayette. Once she woke up, Tara didn't know what to do with herself. She is now adjusting her new life as a vampire.
Nan Flanagan's Death, Bill & Eric's debt to The Authority
There was a period where rebellious activities from vampires spiked. Nan Flanagan happened to have hosted an event, but all the vampires went crazy attacking humans. The Authority sentenced Nan to the true death but before she went to die, she asked Bill and Eric to rebell against the Authhority too or else face the True Death too. They simply killed her.
The Authority promptly captured Eric and Bill. But in exchange for their lives, Bill offered that they find Russell Edgington - who had some how escaped. The Authority let Bill and Eric go, yet they keep track of them as they are monitored with lethal devices. Russell was eventually captured again but then escaped - again - and began leading the Sanguinista movement into new heights .
The Return of Eve & Destruction of the Authority
When Russell was brought into The Authority's custody, Roman kept Bill and Eric there. That is, until Russell escaped again. Following this, more attacks against vampires arose, and the Tru Blood factories were destroyed. The Authority couldn't do much because they were too busy concerning themselves with Eve - the vampire deity slowly seeping into their minds and influencing them to turn against each other for her blood, this included Eric and Bill.
In the final battle, Sookie got word from Jessica about what was going on and decided to go in after Bill. Jason of course wasn't going to let her go alone. At the time, another religious sect of vampires somehow got their hands on an angel (from SPN), and sent the angel to find and attack the Authority. Almost everyone was slaughtered. When Sookie and Jason got there, they found Roman fleeing the angel but Bill sticking around to drink Eve's blood. Sookie, Jason, and Eric witnessed Bill transform into a liaison or manifestation of Eve, shocking the angel. The angel of course had to get Sookie and Jason (humans) out to safety, before this form of Bill destroyed everything.