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Here is the background story, the backstory, up to the beginning of the third series. Lexx is the best science fiction television series to emerge recently but the story can be a bit confusing. I hope to clarify a few points here, although you should remember that you might see things here that you would have preferred not to know until you have seen the episodes. The numbers shown are the episodes that contain the information. For example 1.1 is Season 1, episode 1 (I Worship His Shadow), 2.1 is Season 2, episode 1 (Mantrid).

There are a number of stages in the story:

Humans explore space and colonise different planets.
They meet an alien civilisation, which they call the Insect Civilisation. The Insects are reminiscent of insects from earth but they can grow to an enormous size and survive in the vacuum of space. An Insect also has the ability to pass its consciousness into another creature, including a human.
Insects and humans fight a series of wars and the humans eventually win. Humans from the planet Brunnis 2 lead humanity in the victory.
Unknown to humans one Insect survives and hides itself by burrowing into a planetoid. There it waits. The people of Brunnis 2, the Brunnen-G, become isolationist and pacifist. They develop a new technology whereby they breed captured insect bodies denuded of consciousness which function as machines and vehicles. These may not be the same species as the Insects.
2.1 A group of human scientists explores solar systems and lands on a planetoid. One of the scientists comes into contact with the Insect. The Insect passes its consciousness into the scientist. It knows that it cannot defeat humans in war but it can try to rule over them and eventually destroy them.
Over thousands of years the Insect gradually gains control over more and more humans. It passes its Insect essence from one human host to another as the old one wears out. It establishes a quasi-religious order called The Divine Order, and it becomes known as His Divine Shadow. Millions of humans were loyal to him, unaware of his true identity. The process of transfer of the Insect consciousness from one human host to another becomes ritualised in The Kiss. The brains of previous hosts are removed and kept as Divine Predecessors, inside mechanical devices on top of huge stone columns. The seat of power of The Divine Order is the same planetoid that hid the Insect and still hides the Insect body. The planetoid becomes known as The Cluster, and prisoners are brought from other planets in the empire. When executed parts of their bodies go to feed the Insect body, which grows in size.
1.1 His Divine Shadow destroys Brunnis 2. The Brunnen-G cannot meet the challenge, but one of them - Kai - persuades a few to try. Before battle Kai consults an oracle, who has good news and bad news: the Brunnen-G will be destroyed but eventually The Divine Order will be defeated at the hands of the Brunnen-G. Kai and his comrades attack His Divine Shadow's ship using Stingers (insect-like craft). They are picked off one by one but Kai manages to smash his Stinger into the control pod. He is now the last of the Brunnen-G. His Divine Shadow kills him, but orders that his body is used as an assassin, an animated corpse used to kill His Divine Shadow's enemies. A viscous fluid called proto-blood allows him to function although dead. Proto-blood comes from the Insect body.
Some planets resist The Divine Order. They are the Reform Planets like the Austral B Pair. The 'heretics' plan to grow a new insect-like craft which will become an enormous destructive force, capable of blowing up planets. This is the Lexx.
Assistant Deputy Backup Courier Stanley Tweedle is chosen to carry the amino acid codes for this craft hidden in one of his teeth. Also hidden in one of his teeth is information about the Reform Planet's defensive shields, and information about areas of the universe inaccessible to The Divine Order.
1.1 While returning from a recreational trip, one of the Reform Planets is attacked by His Divine Shadow. Stanley is now drifting in space in his small craft. His oxygen is running out. He is contacted by people who say they will help him. Instead they capture, torture and abuse him. They sell the amino acid codes and the information about the Reform Planet's defences to His Divine Shadow. As a result about 94 Reform Planets are destroyed and His Divine Shadow begins to grow the Lexx. Stanley is not killed in case he has further use and is employed as a Security Guard on The Cluster.
The heretics hatch a plot to steal the Lexx. Thodin of the Austral B Pair and a few accomplices allow themselves to be captured and transported to the Cluster. A miniature flying bomb causes havoc, and in the chaos they free themselves and move towards Lexx. Thodin has the key, his people had to fight a war to get it. The key is in the form of energy which is stored in the body and moves into the hand when required.
On board the same prison ship as Thodin is a woman call Zev Bellringer of B3K. She has been raised by holograms in a box. Prepared for life as a dutiful wife, she is rejected by her husband because she is so ugly. Because she thumped him, she must now be punished by being transformed into a love slave. Due to the chaos cluster lizards break free and one of them disrupts her transformation process. She is made beautiful but is now part cluster lizard. The robot who performs the transformation loses his body but gains the programming that was meant for Zev. As a result he adores her.
Stan gets into trouble over a series of minor infringements and errors of judgement. After failing to report to a correctional facility he becomes a fugitive.
He meets up with Zev and they come across the heretics. The heretics are killed off one by one. Thodin is killed by Kai after passing on the key. The last heretic is killed by a cluster lizard just inside the Lexx. The key is passed to Stan. The ship is so big they have to fly around inside it using a 'moth', an insect-like craft. They find the bridge and the place where Stan needs to stand to control the Lexx. He commands it to move away from the Cluster, pursued by craft led by His Divine Shadow (although His Divine Shadow's brain is removed and kept on the Cluster). Kai regains part of the memory of who he was from one of the Divine Predecessors. He rebels against His Divine Shadow but it is only when they pass through the fractal core that the fight is over and the Insect consciousness returns to the Cluster. They are now in the Dark Zone. The fractal core is like a wormhole that connects the two universes (the Light Zone and the Dark Zone) and Stan had its location hidden in one of his teeth.
After a couple of adventures in the Dark Zone, they decide to return to the Light Zone and the Cluster. Kai needs more proto-blood to allow him to function and they can only find that on the Cluster. They find a very different Cluster from the one they left.
The long term plan of His Divine Shadow was to feed the Insect body hidden in the Cluster, grow it to enormous size, and then transfer consciousness back into it. There came The Cleansing, when all humans from within the empire were transferred to the Cluster, killed and fed to the Insect body. Only a few of the highest of the Divine Order were left alive to complete the transfer. However, they were not all loyal, and the process was disrupted.
Kai and Zev find the dead clerics and the brain of the last Divine Shadow. The brain is in two pieces, one which contains the Insect consciousness. Proto-blood dripping from above reanimates one of the clerics who picks up part of the brain. The Insect consciousness enters him. He resists, but it is too powerful. He is taken into the Insect body which now comes to life. Stan orders the Lexx to kill it but it doesn't work, and so they flee towards a fractal core. The Insect rolls up into a ball and extends a tentacle through the fractal core and penetrates the Lexx. However, an immature cluster lizard that Kai found on Lexx eats into the Insect's brain. It recoils and falls into the fractal core, destroying itself.
2.1 Now back in the Dark Zone they are looking for a home but Kai was infected by the Insect consciousness when he crushed the brain of the last Divine Shadow. The Insect consciousness begins to assert itself and motivates Kai to try to resurrect the Insect species. Kai tells Stan and Zev that he needs more proto-blood and it can only be found by re-entering the fractal core and the Light Zone. He wants to find an immature Insect that could have been one of many growing on the underside of the Giga-Shadow (the giant Insect body). They find one and bring it on board. Kai cannot reanimate it and announces that they must find the scientist called Mantrid who is the only one who can help them.
They find Mantrid but things go badly wrong. They are nearly killed by the reanimated Insect. Mantrid's assistant tries to help his master but his efforts result in Mantrid's being becoming fused with the Insect consciousness. He becomes the enemy of mankind and of the Lexx crew. Mantrid controls vast numbers of drones, which are robotic arms. They can convert matter into more drones and so control more and more of the universe. They increase exponentially in number.
2.2 Zev is killed when evil people try to get control of the Lexx. An alien life form called Lyekka creates a new woman called Xev from Zev's protein. Lyekka is a plant who likes Stanley. She is aware of his dreams and wants to fulfil his fantasies. Xev has the same identity as Zev.
Eventually the whole of the universe is converted into Mantrid drones and converge on Lexx. This causes the universe to collapse. Mantrid is killed but Lexx escapes through a fractal core into the other universe.
3.1 The Lexx needs to eat to be able to function. The crew decide to put themselves into a state of suspended animation because the Lexx is drifting and barely able to function. It cannot even feed itself, there is no organic matter nearby. Eventually the Lexx is in orbit around binary planets. There are people on each planet. They do not have advanced technology and do not understand what the Lexx is. Their most advanced means of transport are balloons. The two planets are so close the atmosphere is continuous although one planet is desert and one all sea. Balloons can pass from one planet to another.
One of the rulers gets on board the Lexx and removes Stan and Xev. They escape but encounter many problems, not least of which is trying to understand the life cycle of the people. When these people die they return as a new adult. There are no children. A few can choose which form they wish to take, and retain their memories. One of the rulers, Prince, can do this and another, Duke, seems to be aware of it. These are rulers of the planet Fire and war against each other and the peaceful people of Water. Now it gets really complicated.

Kai, Xev and Stan

We worship His Shadow. Long may he reign!