How could season 2 and 3 of Heroes

No Maya or Alejandro or Sylar for that matter.
 
Weird title, but if I were to re-write season 2 & 3 I would ...

Season 2

Recast Yaeko .
Have Maya reach New York earlier and have her work for the company.
Eventually have Maya use her power on purpose, with out being all emotional.
Have Caitlin killed on screen
And have more company flashbacks

Season 3
Keep Bob alive!
More Eric Doyle
Change black hole guy's power
 
I think it would of been cool if black hole guys power had something to do with removing air from a place creating a vacuum, which would of course suffocate anyone in that area. He could still accidentally kill someone, but without having a power that's just stupid.
 
Season one:
-bigger finale, as in huge fight (with not so much punching and more powers)
-Sylar being taken away in a bodybag by the Company
-Niki/DL/Micah's storyline would end (flip a coin to whether DL lives or dies)

Season two:
-Maya is no longer a twin, her older brother Alejandro would also be killed during the wedding
-Peter doesn't have the stupid Ireland plot and Nathan is MIA
-West should have a dangerous power and a record that HRG knows about... so that's what him and Claire split about... instead of stupid season one rehash
-Adam still the main bad guy with Elder Parkman as his henchman, and if anyone is tricked into working for him.... mindwiped Sylar (could be used as one of their precious end of show OMGs)
-Re-introduce Arthur during this season.... seeing as it is Generations, have him be gray just like Nathan was but turn out to be the real Nightmare man to setup season three
-Of course.... Hiro in Japan, much shorter
 
I think it would of been cool if black hole guys power had something to do with removing air from a place creating a vacuum, which would of course suffocate anyone in that area. He could still accidentally kill someone, but without having a power that's just stupid.

Unless he's in an airtight space, there's really no way he could be deadly.
 
I love the show just the way it is, but in my mind....

SEASON 2:

-Make it longer, and more in depth (obviously)
-Maya having a HUGE impact in the season finale (it would have made sense and surprised people since she had been traveling throughout the season)
-No Gina
-Less time in Feudal Japan. He should have teleported somewhere that fit with the term "Generations" more besides a way to introduce Adam.
-Having Micah's cousin not being such an idiot.

SEASON 3

-Explanation for Monica or something.
-Niki not dying. I still like Tracy though, she rocks.
-Maya not losing her power.
-Sylar not having so much background. I liked him as a simple clock maker who's powers didn't turn out so well.
-More Molly. I like her character for some reason. Well, i also like Maya and Tracy so that might not mean much to you critics.
 
kill more people

leave sylar evil as we all like him.
 
Said it before, say it again:

Season 2
Give Peter's amnesia-kaitlin-whats in the box-paint the future-get chased by Elle-lose Kaitlin-get duped by Adam storyline to Gabriel Gray.
Let Matt and Nathan be dead. Subplot where Candice replaces Nathan in his life and eventually 'becomes' Nathan, even in her own mind. Matt Parkman Jr. becomes an important baby for some reason or other.
Feature the 12 as the focus of the paintings as opposed to HRG. Set Peter and Monica (granddaughter of one of the 12) on the discovering the twelve storyline that Matt and Nathan had, and lengthen it.
More action in Feudal Japan, including Hiro learning sword fighting. Hiro and Adam split when Adam wishes to take over Japan so that he can use to to save (take over) the world. To remove Hiro from comic relief world, less Ando for now.
I'd put Mohinder, Jessica, Molly and Micah in Mohinder's apartment together, just trying to get by and live a normal life... y'know, except for Mohinder trying to take down the Company. Mohinder would betray those three, not HRG.
Maya and Alejandro would replace Hiro and Ando as comic relief, and would meet people along the way every episode (ie Meredith, Claude, Micah, a new guest star, perhaps someone from the online comics, one of the 12, Candice/Nathan, etc)
Claire would trust West, who would betray her to the Company eventually.
Include the "1975" Flashback ep.
Build up to a battle between the Original Generation (Adam, Bob, Angela, a Kaito-possessed Ando, and one more) and the new generation (Peter, Sylar, Claire, Monica and Hiro) - The OG have lesser powers but know how to use them a lot better ie Angela using her precognition as spidey-sense, Bob transmuting air in front of him into a diamond barrier, etc...

Season 3
Go a completely different direction, either do the Virus storyline in full.
Or do "Villains" like "Heroes," that is, ordinary people with extraordinary abilities who end up, through various vices, weaknesses and failings, trying to take over and destroy the world instead of trying to save it. Do six new "villains" who start out as just waitresses, cab drivers, firemen, physicians, gamer teenagers and retired bookies.

If we HAVE to follow the way they went, then the jailbreakers would all be utterly badass and at least 4 would have real depth. Sylar would be more of a pent-up animal the Company uses than someone who reformed and stuff. Claire would be teamed up with someone else, likely Mohinder or something. Hiro would be traveling throughout time, interacting with other characters similar to how LOST flashbacks and flashforwards work, where he weaves in and out of others' storylines, giving all of us a bigger picture of the universe and the connections. The would be no 'powers formula' storyline ,and the 'villains' would be doing nothing short of taking over the world 'for its own good.' Gabriel would obviously not be a Petrelli, there would be no Tracy, Elle would still be a psychopath... y'know, don't break the universe-type stuff. They symbol would still be everywhere (not just on people's logos, but in the background of stuff) and there would still be that ubiquitous "Hero" being tossed around dramatically.

And as a bonus:

Season 1
For the finale, the six combatants would encircle Sylar, he'd redirect both Matt and Claire's bullets back at them, Sylar blasts Peter into Nikki before dodging a slice from Hiro, freezing his face so that he has to claw at it, and making an ice puddle under his feet so he falls on his back. When Sylar goes to blast Nikki with radiation, injured D.L. grabs his heart. Sylar soars backwards and DL lets go as he flies through a wall. Peter gets Nikki's superstrength and tells her to go protect the kids and begins to Wallop on Sylar, Peter's hands glow and he looks at them all terrified. Sylar laughs and begins talking about how Peter is the bomb and how Sylar came here to stop him because "You're the problem Peter. I'm just the bad guy." and proceeds to try and choke the life out of him. Hiro interupts and before Sylar can kill Hiro, DL phases into his body, holding him in a seizure and calls for Hiro to strike. After a short protest, Hiro does so, killing D.L. and apparently killing Sylar (cue Micah: "Daaaaaaad!")
Peter's meltdown then continues as it appeared.

Also, I'd imply, say by Charles Deveaux, that there are different kinds of time travel, "that Nakamura boy's already done two or three." to explain why Hiro's Five Years Gone time travel rules are different from his "October 2, November 8" time travel rules...
 

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