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Andy returns from earth with a large crate of alcohol that restores peace to the ship for a while.

The Blue Dwarf's sensors read massive amounts of enemy ships approaching. Fighters are scrambled, later to find it's a trap to get most people off the ship, whilst Boris Vasquez's gang can take over, planning to sell the Blue Dwarf on eBay. The Blue Dwarf jumps away, leaving the stranded crew to take shelter on a planet inhabited by Xenophobic and unwelcoming Turtles called "Shellites".

The crew on the planet live amongst the Shelites and try to stay hidden in an underground base.

Only Andy, Rufus, Rosette and Efof manage to stay aboard the Blue Dwarf where they start gureilla attacks against the pirates.

The crew on the planet find and take over a new Shellite ship, and fly it back to the Blue Dwarf, along with all the Starbugs and Blue Midgets containing the Blue Dwarf crew. The Blue Dwarf is liberated and the crew return to duty.

Andy hacks into planet eBay with the help of Rosette, a seemingly impossible task. In doing so Andy Roos reveals that he is the mega-corporation killing hacker named "Hal" and thus drawing the attention of the Space Corps. With the help of the Captial ship 'Oath-keeper' the Blue Dwarf is liberated and the crew return to duty... for all of five minutes before...

Captain Calvert receives orders for the Blue Dwarf to return to Earth to be re-crewed, and everyone aboard fired. Calvert refuses to follow the order.

Jed plans to turn the Blue Dwarf into an intergalatic casino. To help further this goal he dispatches resident Spy and Hacker Rosette and Andy to disrupt the escorting Pink Dwarf Nursing vessel. In the effort Andy creates a holographic backup of his mind. (As of september 2008, this hologram becomes Dysart).

Captain Calvert is shown a dark version future by a mysterious time traveller named "Annie", and says this is what will happen if he refuses to comply to orders and take the Blue Dwarf back to Earth. Jed is still not convinced and refuses to surrender to the Space Corps.

The crew mutiny against Jed and call the SpaceCorps ship "Oath-Keeper", which arrives at high speed and crashes into the Blue Dwarf. The crashed ship leaks a high-density unstable gas called cyclosium B into the air of the Blue Dwarf, causing something bizarre to happen to the males of the crew. Their penisses fall off, and try to kill people.

A time-traveller from another dimension named "Potential" and collegue of "Annie" encourages Andy Roos to shoot Jed Calvert. Jed is just about to finally send a message to the Space Corps that he will surrender when Roos shoots him. Calvert leaks green blood out of his wound much to everyone's surprise, as no-one had any reason to believe he was anything but Human.

The Blue Dwarf is towed back to Earth and the crew are given different jobs on new starships, or other places across the galaxy. Some are assigned to the SCV Dauntless, a spacecorps ship.

Planets around the galaxy start to be attacked and wiped out by a new type of alien called the "Krylons". These are robots with an agenda to rid the entire galaxy of non-robotic life.

The unmanned Blue Dwarf is sent via remote-control through a Krylon gateway called the "Firewall", which leads to the Krylon dimension. The Firewall destroys all organic life that passes through, so the Blue Dwarf passes through without a crew. It's aim is to send data back.

The SCV Dauntless is shot down on a rocky planet and the survivers and ex-Blue Dwarf crewmembers have to fight the Krylon troops on the planet.

The mother of Seymour's baby, Jenny Bond goes missing, despite her still being in a coma since the Scutter rebellion. His daughter Alota Niples also goes missing. A mercenary working for TransMed Pharmacuticals admits to kidnapping baby Alota, but not Jenny. TransMed pharmacuticals also kidnap Jed Calvert who has been in a coma since he was shot by Andy Roos. 

The ex-Blue Dwarf crewmembers on the planet find a long-range transporter pad which leads to the Mollopod homeworld where an alliance is drawn up with the Humans, Mollopods, Aeron, Eniram and the Anti-noptera to help each other fight the Krylons.

Andy Roos reveals that he is the hacker named "Hal", he encounters the Krylons and he and Kara discover that the leaders of the Krylons actually resemble penguins.

The Mollopod capitol city is attacked by Krylon robots, and the Blue Dwarf crew defend it.

Justin befriends a shapeshhifter called "Melchwimp" on the Mollopod planet. Melchwimp helps Justin and Seymour fight the Krylons.

Andy Roos and Kara take control of the starship Axolotl and use it to bombard the Krylon forces on Mollopod from orbit.

The fighting on Mollopod stops and various starships from all the alien races in the Alliance regroup around the planet.

A Krylon robot called "Claude" that Jay had known since his clone Jayne had come aboard gave them information about a Krylon base on a moon called "Kraxor". Kraxer was a volcanic planet that had an important Krylon factory on it.

Seymour and Justin take a transporter to an area of Mollopod where someone had seen Jenny alive. Melchwimp is killed by mistake by an Eniram.

The factory on the Krylon moon "Kraxor" is blown up. This causes lots of volcanos to erupt and the crew have to get to safety.

Seymour discovers that his ex-girlfriend and mother of his child is an alien from another dimension.

The crew are all turned into holograms and given a holographic ship to control, the "Enlightenment v0.22 BETA". This allows them to pass through the Krylon gateway without being killed and to enter Krylon space. Also providing that their holographic ship is not destroyed, they will be invincible. Their real bodies remain in a hospital on the Mollopod planet.

Once in Krylon space, their holographic ship is boarded. They repel the Krylons by firing an assortment of holograms at them.

AI programmer Lester and his pet Id, SNIDE, assist in the repelling the attack. Thanks to his knowledge of artifical intelligence he manages to help repel the assualt. (As of September they where hired aboard the Blue Dwarf full time.)

Andy Roos, an accident causing leaving his heavily damaged body with only hours to live, digitizes his mind and skips across the holographic battlezone. Managing to get into the Krylon's central mind, he sacrifices himself to destroy the Krylon's connection with each other. This makes the Krylons useless but Andy Roos dead.

The holographic backup of Andy Roos upon the Pink Dwarf, taking the new name of Armend Dysart, is arrested as an illegal AI and is incorporated into a experimental robotic body.

The Krylon ships explode, damaging the core of the SS Enlightenment v0.22 BETA slightly, reducing them to emergency power mode. This shrinks the ship to only a few centimeters tall. They locate the Blue Dwarf and fly their tiny ship around the Blue Dwarf, passing through a small alien creature on the Promenade first.

The holographic crew pilot the Blue Dwarf back through the Firewall into normal space, to meet up with their bodies on the Mollopod planet. But an Amnesty International spaceship commandeered by Bob Geldoff clone #388 threatens to fire missiles at the Mollopod planet. The Blue Dwarf arrives in time to save the planet and everyone is restored to their real bodies.

The Blue Dwarf is restored with it's normal crew, but with the addition of Jay Chrysler as Captain to replace the missing Jed Calvert.

The memory of Andy Roos is incorporated into a robot called Dysart.

A problem with the Blue Dwarf's Kinetically Neutralised Octagonal Battery causes hundreds of multiple Blue Dwarfs from alternate dimensions to be dragged into our dimension. Crews from the original Blue Dwarf travel to the others to fix their Kinetically Neutralised Octagonal Batteries (K.N.O.B's). The crew meet themselves and friends from alternate universes.

A Blue Dwarf captained by Jay's dead wife Alota appears, and is followed by Evil Jay's ship the Thorax. The Hymenoptera start boarding and attacking all other Blue Dwarfs, to capture every alternate of Jay Chrysler for some currently unknown reason. 

Dysart is immediatly put to use searching and rescuing JMC officers Kara and Keto. Both of which where trapped aboard an 'evil' blue dwarf.

Lester and Dysart encounter one another back aboard the original blue dwarf and team up shortly after. Lester, who is having a 'slight' personality crisis, assists Dysart in assualting the Thorax and saving the JMC Officer Jayne.

In the counter attack Dysart held the shocktroopers back while Lester pulled back with the escapees.

Evil Jay realises he needs to capture Jay from out universe who is the only exact genetic match as him. Now that all the many other Blue Dwarf's are useless to him, he instructs his Hymenoptera army to kamikaze bomb the other ships to destroy them.

Lester decides he's had it with this mother#$#%ing hymies on this mother#$#%ing plane and attacks the thorax' brain itself giving enough time for Jay to confront Evil Jay on the Thorax. He leaves him to die when he crashes Alota's Blue Dwarf into the Thorax.

Justin Pancake is convinced by himself from another universe to help the Hymenoptera. He is taken to see the “General” who turns out to be Jed Calvert from another universe, but is half-Hymenoptera. Calvert dies when he falls on some whiskey and dissolves. 

Blue Dwarf is finally restocked with skutters, peewees, guns, fuel and most importantly- booze. There was much rejoicing. Additionally, after more than a year of grime a mongol's horde of elite human Janitors are freshly hired. Sanity optional.

Seymour visits Queen Brittany on Planet New Tenerife to convince her to help him rescue his baby from TransMed Pharmacuticals. Lester Seventeen-dot-Phelps visits the same planet separately and takes on Seymour's identity to use his credit card. Lester gets in trouble first with customs, and then with an Assassin meant for Seymour.

Rosette travelled to the TransMed Pharmaceuticals building on Earth to assassinate Jed Calvert who is there being experimented on. She discovers that Jed is a “Hymenthrope” - a being that can turn into a Hymenoptera bug without warning. She ends up releasing him and both of them travel back to the Blue Dwarf, where Jed kills several people in his Hymenoptera form.