I just want to say: listening to Tom and Cory recap HEROES is vastly preferable to actually rewatching it.
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I would note that HEROES and FRIDAY NIGHT LIGHTS in 2007 were dealing with different narrative situations. I'm not super-familiar with sports, but I assume that sports matches and a pandemic are events that take place on pretty different scales. It may work for football games to happen offscreen. That wouldn't work for an end-of-the-world situation (although MILLENNIUM tried to wrap up a global pandemic between Seasons 2 - 3 and to laughable results).
HEROES had planned a 24 episode arc for Season 2: the first 11 episodes were Volume 2, "Generations", and revealed that superhumans, including Sylar, were becoming infected with a debilitating virus. Peter and his girlfriend Caitlin (Katie Carr) accidentally visited the near future in which the virus had begun infecting normal humans, and 93 percent of the human race had died. Peter lost control of his time travel powers and was sent back to the present before he could bring Caitlin back with him. Episode 10 revealed that the legendary samurai Takezo Kensei, also the immortal known as Adam Monroe (David Anders), had created the Shanti Virus as a means of population control and sought to unleash it. Monroe would later goad and taunt Peter that the woman he loved was trapped in a terrible future.
"Generations" was to end with Episode 11 in which Peter would fail to stop the virus from breaking out, heralding the future he saw and in which Caitlin was stranded. The town of Odessa, Texas would be quarantined. Nathan, announcing the situation to the press, would fall ill and collapse.
Then we'd have Volume 3, "Exodus", across Episodes 12 - 24. The heroes would try to contain the virus while Peter would trying to regain control of his time travel powers before changing the future, so that he could save Caitlin before that future timeline was erased.
When the HEROES creators realized that they would have to stop production with Season 2, Episode 11, they were facing a difficult situation. Due to their shooting schedule and contractual agreements, even if the strike were resolved, HEROES would be filming Season 3, not the second half of Season 2. The viral outbreak storyline was not something they could cover with a time gap and references to offscreen events. It needed to be a current and immediate situation if the story were to be told at all. Also critical to the story were Caitlin and Adam Monroe, which was another problem.
With the strike and the hiatus, HEROES had lost full access to David Anders, whose Adam Monroe was intended as the primary villain of Season 2. And HEROES' contract with Katie Carr to play Caitlin expired as well, and my understanding is that once Season 2 shut down, Carr was travelling between the United States, England and Australia, engaged in a modelling career and studying screenwriting in London. The bookings and studio sets HEROES had made for locations to render the viral quarantine of Odessa, Texas were also lost.
They'd lost the ability to use David Anders as the primary villain, they'd lost Katie Carr, they'd lost their preproduction work, they'd lost the immediacy of following up on Episode 11 a week later. With all this, the HEROES creators felt it simply didn't make sense to end Episode 11 on a clifffhanger and do the "Exodus" viral outbreak storyline in Season 3 in 6 - 12 months' time. They had no way of following up on it properly with all their losses.
If they'd done "Exodus" for Season 3, they would have had to write David Anders out with minimal appearances; they would have been unable to feature the Caitlin character significantly or at all. They would be following up on a viral outbreak cliffhanger that had aired 10 months ago, losing the opportunity for Season 3 to offer a clean and clear jumping on point for viewers as is expected for the season premiere of a major network show.
Given the multiple characters and arcs unfolding simultaneously in Season 2, it was a lot to ask a 2007 - 2008 audience to remember. HEROES was only available to stream via NBC Direct for US residents and wouldn't be available on iTunes until 2009.
Even as recently as 2021: I watched THE FLASH where the first three episodes of Season 7 were devoted to the mirror dimension plotline of Season 6, a season that had been cut short due to the pandemic hiatus. Like HEROES, THE FLASH was off the air for 10 months. Unlike HEROES, THE FLASH didn't (and couldn't) wrap up its truncated season and had to devote the first three episodes of Season 7 to resolving Season 6.
I was a devoted fan of THE FLASH, and I watched Season 7's first three episodes with great confusion. It had been 10 months since Season 6 and I had largely forgotten all the details of the storyline. I couldn't remember who Eva McCulloch was or what she wanted or how the artificial speed force tied into it or how mirror duplicates were involved. I couldn't remember. And I was too busy to rewatch Season 6. Due to limited recall, THE FLASH's sixth season opening was baffling to me.
And THE FLASH in Season 6 had a lot less going on than HEROES of Season 2, so I would posit that the average viewer would have found Season 3 of HEROES even more confusing than Season 6 of THE FLASH had HEROES attempted to do the "Exodus" storyline 10 months delayed.
I think the HEROES team saw that the virus plot was not something they would be able to follow up on effectively, so they reshot Episode 11 slightly so that Peter would stop the virus, and the replacement cliffhanger wouldn't require the audience to remember the Shanti Virus storyline when Season 3 premiered.
And on the whole, the creators' predictions seem to have been pretty accurate. David Anders was tied up with an independent movie when Season 3 started and had to be written out fast; Katie Carr was, I believe, in Australia. Ignoring Caitlin was a bad option, but there were no good (or available) options to bring her back.
From a writing standpoint, it was also difficult to address the emotional fallout of Caitlin's lack of fate. But the strike made it impossible to film anything new with Katie Carr for Episode 11; even if they attempted to save her with dialogue referring to her being offscreen, how could they save her from a timeline that was gone? Given that Peter couldn't control his time travel powers and was fighting Hiro at the end of Season 2, what options had there been to resolve Caitlin's storyline before the virus future was revented? Addressing Caitlin was a problem; ignoring Caitlin was a problem. HEROES is about ordinary people in extraordinary situations. Peter Petrelli's character is defined by his empathy and how he connects with people, reflected in his power of empathetic ability replication. Caitlin is an ordinary person, so leaving her in a horrific future undermines HEROES' entire mission statement.
Caitlin is an innocent person whom Peter loved, so Peter not saving her undermines Peter's characterization. Peter would either seem callous for dismissing her situation or be shattered by his inability to return to that future to save her, which would tie his character up in a distant storyline. As a result, the writers made the displeasing -- but understandable -- decision to simply never refer to it again: to bring it up would either undermine Peter or overcomplicate Peter. Their expectation was that when Season 3 premiered in September 2008, the majority of the audience would have forgotten about Caitlin, a character who had not been seen onscreen since November 2007, almost 11 months.
So, there were really no good options here: ignore Caitlin and move on from the virus plot and seem callous to anyone who remembered the character. Focus on Caitlin and the virus plot and Season 3's first impression would be that it was still mired in a storyline that, without immediacy and recent memory, was now difficult to follow and remember and also difficult to film due to losing the guest actors.
They chose to ignore Caitlin and hoped the audience would too... and I can't say the alternative would been any better. So I forgive the writers for choosing the simplest bad option over the complicated and confusing bad option. And I think they forgave themselves.
What HEROES should have done, however, which they never did -- they should have devoted one of their many webcomics to resolving Caitlin's story so that fans who did remember and care about Caitlin wouldn't think poorly of Peter for never mentioning her again.
I would note that the Charlie character (Jayma Mays) in Season 1 was really beloved as Hiro's love interest. She even inspired a tie-in novel, SAVING CHARLIE. But Charlie's character was unsustainable for the show as a regular, and she died a terrible fate. She wasn't mentioned in Seasons 2 or 3.
And yet, the HEROES creators brought the character back in Season 4 to give her a (somewhat) happy ending. I think they would have liked to do something similar for Caitlin... but how?
I imagine the reason the creators didn't at least produce a comic book is because with the viral outbreak timeline having been erased, the writers were at a loss for how to even find Caitlin. Even in a comic book: how were they supposed to get Peter back to that future timeline that was no longer available, even to a time traveller?
I myself have needed 17 years to come up with a solution...