Captain Scarlet/WMG

The Mysterons are preparing humanity to face a greater threat.

Think about it. Very few of the Mysterons' attacks would have caused any great loss of life even if they had succeeded. None of their plans would have killed more than a few thousand people. Considering that the Mysterons have supposedly declared war on the entire human race, they don't seem to be trying hard.

But the threat of the Mysteron attacks has forced humans to develop extremely effective defences and countermeasures. (This is assuming that Spectrum isn't the only organization fighting the Mysterons.) These will be needed when the real evil alien invasion turns up. The Mysterons are sinister but ultimately benevolent Well Intentioned Extremists.

• Also, the Mysterons deliberately turned Captain Scarlet into an indestructible man, and then allowed him to go free when he proved that he had Heroic Willpower. They are hoping to produce as many of these supersoldiers as possible because indestructible men will be needed to defend Earth later on. But all of the other indestructible men and women have so far proved disappointing. None except Captain Scarlet have the Heroic Willpower required.

The Mysterons don't care about the war.

They're just messing with humans for their own twisted amusement. It's all a game to them.

There are no Mysterons. It's all done by computers in their city, after they abandoned it or died off.

This one has been kicked around in the fandom for years, and there's a certain amount of circumstantial evidence for it.

We never see a Mysteron. We see their agents, recreated from objects and people that they've destroyed; but every shot of their complexes, on Mars or on the Moon, is empty of any visible life-forms. We hear "the Voice of the Mysterons" in the original series, but that title only means that it makes "official" pronouncements on their behalf; it might be the AI equivalent of a modern American flying a Confederate flag.

It would explain the odd strategy that the Mysterons use. Their stated aim is the destruction of life on Earth. But they concentrate on psychological warfare, which can only affect the sentient life and cannot directly kill anything. They always give their enemies a chance to stop them. They use the minimum number of agents required to accomplish the current job. With their powers, they should be able to crack the planet open without much trouble, and yet they play psychological games. Perhaps they are limited in what "they" can do by previous programming?

Similarly, if a plan is thwarted, they don't keep trying. They may have a back-up plan, but otherwise they move on to a new target. This argues for limited flexibility, such as one might get from a computer. (Remember that this is a 1960s series, and computer programmes weren't as versatile as they are today).

A final point in favour of this argument is Captain Black. He is their primary agent after they killed and recreated him, and their control over him is as complete as possible. Presumably, they know his every thought and memory. Yet they continue their war on Earth, which was started as revenge for his attack on their complex, an attack made in a moment of panic. Even if they didn't bother to find out why this human shot at them, one might expect them to check after Colonel White broadcasts a message to them using a communications crystal taken from their Lunar base which explains that the attack was a misunderstanding and asks for peace. But no, they blow up the crystal in an attempt to destroy Cloudbase. Either their psychology is so alien as to prevent them from understanding human behaviour, or their responses to attack are fixed. Either of those can come from an AI.

The CGI series and the Supermarionation series take place in the same reality

One of the Compilation Movies show that Mysterons are capable of turning back time. The final episode of the CGI series has Captain Scarlet appear to blow up the Mysterons' lair, only for it to be revealed (to the audience) that Captain Black and the Mysterons are still at large. Angered at their defeat, the Mysterons decide to turn back time and start all over again, giving rise to the Supermarionation series.

Captain Black wasn't destroyed and recreated. He was merely inserted into the new timeline by The Mysterons.

• Um, how are you going to explain how at the beginning of the supermarionation series, Captain Black is under his own control?
• Communications blip? If you carried a cell phone to a time before cell towers, it wouldn't matter if the phone still worked otherwise -- you couldn't make calls with it. If you took a modern cell phone to a time when all cell phones were analog, you'd probably have the same problem. That's what it would be like: the Mysterons had to reestablish, and maybe retroactively replan, their communications tech, and then take Captain Black over all over again.

It was Captain Black all the time

Notice how CB speaks just like the "Voice of the Mysterons."

He's always there, even if it's just to tell an agent, "You know what to do."

There are no Mysterons. It's just him. Presumably he found an abandoned alien (not Mysteron, he made up the name) base on a previous expedition, took control of it and, for reasons best known to himself, decided to use it to wage war on mankind.

Or maybe this is his idea of a practical joke.

The whole incident in episode 1 was staged by him as an excuse to declare war. It's all done with recorded messages and remote controlled or programmed devices.

The guns in Captain Scarlet contain electricity in the bullets

at some point prior to the episode where it was discovered that electricity was the mysteron's achilles heel, Dr Giadello (the guy who invented the mysteron gun and camera) ending up being assaulted by a Mysteron clone then threw him into an electric curcuit. from there on he started placing electricity in spectrum's guns' bullets secretly through unknown means.