Segata Sanshiro was deliberately assassinated
The missile attack on Sega's headquarters was intended to draw out Segata Sanshiro, who the perpetrators of the launch knew would sacrifice himself to save his beloved Sega. The only way to kill Segata Sanshiro was to force him to deflecting a missile barehanded, ride that missile out of the atmosphere, and explode in space - anything less wouldn't have stopped him. Who had the most to gain from slaying Sega Saturn's incredibly awesome mascot?
Sega couldn't make consoles without Segata Sanshiro
Segata Sanshiro's awesomeness is what fueled the company for years - it took Sega years to recover from his loss.
- The loss in morale from Segata Sanshiro's sacrifice saving Sega headquarters contributed to the company's decline.
Segata Sanshiro isn't dead
He's Just Hiding. Sanshiro only caught a missile barehanded, rode that missile out of the atmosphere, and exploded in space...that's completely survivable - right?
Segata Sanshiro will return...
In his own video game.
The missile in the final commercial was launched by Nintendo.
As the final move of the 1990s console wars, Nintendo decided to destroy Sega. But it wasn't to win the war.
Nintendo knew that the N64 was losing badly to the PlayStation, and in their hearts, knew that the PS2 would beat their new console, the Dolphin (codename for the GameCube), and decided to take them down with them.
When Segata redirected the missile, Nintendo knew that the Dreamcast would fail, so they stepped up their game with the GameCube, churning out a decent console that didn't do so well because everyone thought it was a kid's toy. Meanwhile, the Dreamcast failed miserably, and Sega became a third-party developer.
An explanation on how Segata 'survived' the explosion
Segata was eventually
confirmed to survive 14 years after he was allegedly killed by
the exploding missile in the final commercial. How? Simple. There was no explosion.
So why do we see it anyway? In reality, the employees, assuming the worst, believed that Segata rode the missile to his death, where it would eventually explode and kill him. But nobody was actually around to witness it. It seems that by sheer awesomeness alone, Segata managed to tame the missile and survive, without eating, drinking, and oxygen for all those years.
Segata was bitten by those zombies... who became Segata Sanshiro clones in the following commercial.
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