In the future Matt and Daphne are married and have a daughter and also raise Molly. Molly helped Daphne locate Peter. That is how Claire knew he was in Costa Verde and Knox sensed that Daphne is scared of Peter.
Peter discovered that Gabriel lived in Costa Verde from Mohinder after reading his mind. Mohinder has mutated more and keeps himself covered by a robe and doesn’t want anyone trying to look at him. He lives in the loft that belonged to Mendez. The house that Gabriel lived in was the same house Claire lived in when the moved to CA. In the future Nathan becomes President of the US and Tracy is the first lady. He gives a speech about the tragedy in Costa Verde killing 200,000 people. The African tells Matt that to end his journey he must find his totem (an animal in this case to guide him), Matt leaves the hut and sees the same turtle he saw when he first arrived and starts to follow it.

HRG and his new partner go to a local bank heist with four villains; including Peter being trapped in one of them. Hiro and Ando track Daphne to Germany, and meet the Haitian. Tracy Strauss goes to New Orleans to find out more information about Nikki. Meredith teaches Claire a lesson about fighting. Usutu shows Matt a series of paintings about him

Sylar goes to the Company and inadvertently releases 12 super-powered criminals while Claire learns more about her powers. Meanwhile, Hiro and Ando travel to Paris to track down the speedster who robbed them

Peter is running. It’s four years in the future (says a title card) and someone has a gun pointed at him. It’s Claire, and she’s looking brunette and pissed off. They have their differences now, and Peter seems to still be on the good guys’ side. After a brief exchange about what’s right and wrong, Claire pulls the trigger. Silly Claire! Peter stops time, side-stepping the bullet and nearing a frozen-in-time Claire. When suddenly–

Flashback to present day. Peter just time jumped to Nathan’s press conference in season two. Holy crap, Peter just shot Nathan. He was the gunman from last season. Now present-day Peter is after future Peter (who wears a wicked scar on his face) as they run through the building. Confused yet? Future Peter escapes (at least we think he did).

What appears to be present-day Peter rushes Nathan to the hospital, where his brother’s life hangs on the line. Here comes the doctor to tell Peter that– Nathan is dead. Or is he? Nathan springs to life after Peter kisses him on the forehead. Is there anything Peter can’t do?

Hiro is goofing around with a clock, stopping and reversing time. Hiro is the boss of Yamamoto Entertprises, and he’s loaded. (With money, not booze.) Ando and Hiro have a great exchange that elicits laughs, and Hiro says he’s bored. Perfect timing–a message from Hiro’s dad is delivered to his office.

Sylar visits Claire, and does not eat her brains.
Claire is at home, and OMG it’s Mr. Muggles! Enter Sylar (yes!), who surprises Claire. But Claire has a surprise of her own as she clocks him in the head. She tries to escape but all the doors close. Does Sylar have his powers back? Claire has a knife and Sylar is stalking her. This scene looks like Scream.

Maya and Mohinder are at his apartment and he thinks he knows how to control everyone’s powers… through the adrenal glands.

Hiro’s father’s message tells him he has a destiny, and part of that is to never open a safe that holds several secrets, including Hiro’s path. Doh! Surprise… a curious Hiro opens the safe immediately. And inside is another video, with Hiro’s dad telling him, “I told you not to open the safe!” The crowd erupts in laughter. Inside is a molecular formula, which gets taken from his hands by a blur before Hiro can comprehend what it means. The “blur” has gotta be the Speedster, the newest cast member… Hiro stops time and follows the blur’s blur, with what looks like Heroes best special effects yet. It is the Speedster, and she is immune to Hiro’s time-stopping power (or at least it slows her down to regular speed). After an exchange, she pops him in the face, time resumes, and she bolts with the special formula.

Back at the building where Nathan was shot, future Peter (who can change his appearance to that of present-day Peter) encounters present Matt Parkman, and he gets busted trying to tamper with the scene. The two have some crazy mind-reading standoff, then Peter then tells Parkman he’s seen too much and zaps him out of existence. Matt simply disappears… that was Peter’s coolest trick yet.

Nathan walks out of the hospital to a church. He’s found God now, it seems, and delivers an Obama-esque message of hope.

Mohinder thinks he’s isolated something that controls powers.

Sylar is still at Claire’s, and Claire knifes him in the chest. Ouch. He manages to pin her against the wall, and does the old finger cut on her forehead. Oooooh! Now he’s playing with her brains, trying to get her power to regenerate before he bleeds to death. “Are you going to eat it?” Claire asks, referring to her brain. “Eat your brain? Claire, that’s disgusting.” Well that answers that question. Sylar now has Claire’s ability… this does not bode well for our boys. Sylar gives Claire her scalp back and lets her live, saying she’s special and different and that she can never die. “And now I guess neither can I.” Bone-chilling! But for those of us who love Sylar, simply awesome!

Mohinder is getting all Dr. Frankenstein on Maya, saying he wants to inject himself with powers. Maya says it’s a curse, but that’s because her power is a real drag. She asks him to destroy the formula. I don’t think Mohinder thinks that’s a good idea.

Nathan is really getting religious on Peter now, saying they can all be angels and that he’s been touched by God. Peter leaves, and Nathan gets another visitor. Uh oh, it’s Linderman. He’s back, and he has a beard.

Nikki’s first appearance is in lingerie, thank god. She’s going by the name Tracy and she’s someone’s toy.

Matt wakes up in the desert with a scorpion on his face–yeah, he’s confused.

Hiro jumps to the future to see what destroys the world, and he sees Japan in a panic. He also sees himself talking to Ando, arguing about the formula. Hiro is ready to strike with his sword, when Ando busts out a street fighter fireball and decks Hiro. Ando! With powers! The sky opens up and all hell breaks loose, and Hiro jumps back to the past/present. If Kring and company can keep this up all season, I’ll be converted.

Mohinder is on the docks, and he’s juicing up with the formula. He convulses and we cut to…

Momma Petrelli visiting Nathan. Mom knows that Peter here is future Peter. In the “Company” headquarters, a bald man says he’s Peter Petrelli–did future Peter pull some sort of Scanners trick and put present Peter in someone else’s body? HRG is also locked up, throwing a ball against the wall in an obvious reference to Steve McQueen in The Great Escape. Some of our Heroes are in really bad shape.

Mohinder is getting mugged. But this isn’t normal Mohinder. He can now beat some butt, and he loves it. It’s unclear what his power is, but he can bend a gun and throw a dude 50 feet. Good for him! It’s about time he got some props.

The show ends with “HEROES CONTINUES…NOW!”

(Courtesy of TV.com’s Official Recap)
http://www.tv.com/story/11517.html?&page=2

In Texas, Peter faces off against former friends due to Adam’s misleading story about the Shanti virus. Micah enlists the help of his mother to rescue Monica. Maya is shocked when she learns the truth about her new friend Sylar. Elle tries to make her father proud.

After tracking down the woman in the company photo, Peter travels to Primatech in Texas to destroy the virus, but not everything is what it seems. Hiro continues the pursuit of his father’s killer. Niki is reunited with Micah, and Claire deals with the aftermath of her father’s death. Finally, Maya has to choose to remain with Alejandro, or go with Sylar.

Mr. Bennet prepares to move his family when he thinks the Company has found them, but Claire doesn’t like the idea. Hiro returns to the present and upon discovering his father’s death, travels back in time to stop it. Meanwhile, Matt works to master his new mental abilities.

The events of the “missing four months” are explored. Maya and Alejandro must go on the run, it is explained how Peter ended up in Ireland and what happened to Nathan, Niki, and D.L

Peter and Caitlin learn about the endstage effects of the Heroes virus. Many of the Heroes work together to fight the Nightmare Man. West is shocked when he discovers the identity of Claire’s father. Hiro and Kensei’s journey comes to an end.

Peter goes on a search. West convinces Claire to stand up to someone. Hiro struggles with his feelings for Yaeko. Suresh has more problems with the Company. HRG tries to locate more of Isaac’s paintings. Alejandro doesn’t trust Sylar.