The year is 2201, one year after the Star Force returned to Earth with the CosmoDNA which removed the Gamilon radioactive pollution that was threatening all life on the planet. The Comet Empire prepares to begin its assault on unsuspecting Earth. We learn that Desslok of Gamilon is still alive, and in league with the Comet Empire. Most of the Star Force crew members are now on Earth. The Argo (with Wildstar and Homer) is returning from remote patrol duty in the solar system. On the way back to Earth, the Argo receives an encoded message amidst a huge electromagnetic power surge. It is not yet known whether the surge was used to send the message, or to jam it, or for some other purpose. During the surge, the Argo is attacked by an unidentified squadron of fighter planes. With its radar damaged, the Argo has a near collision with the new Earth Defense flagship, Andromeda, which refuses to give up its flight path for the incoming Argo. The two ships scape by each other, and the Argo lands on Earth.

Sandor and Wildstar visit the new shipyards, and discuss many of the new tech improvements going into Earth's new fleet. The Andromeda and other ships have skeleton crews, with most of the central systems controlled by computer. Sandor laments this since he believes that "we must keep control of the machines we create. If we don't, we're doomed." (see episode 1-18). There are improvements for the Argo too: New shock cannons that have an increased range (150% of the original); and, a time radar that is capable to detecting past events in space. Sandor demonstrates it for Wildstar by showing Chief Engineer Orion urinating against a ship-yard wall. Must be getting old, that one. But, all the improvements are not welcome. Sandor reveals to Wildstar that Earth Defense Committee wants the Argo to be adapted to the same kind of computer control system a la Andromeda. Derek flies into a rage and storms off to the Commander's office in protest. He urges, "The Argo's heart and blood is the Star Force. It's people, not machinery!" While pleading his case to the Commander, as if in symmetry to the recent power surge, there is a power blackout over most of Earth, which is an attempt by the new enemy to soften up Earth defenses. During the outage, Wildstar spots an alien spy plane (a horseshoe crab-shaped bomber) flying over the darkened city. Sandor notices a huge comet in the distant sky heading towards Earth. He and Wildstar analyse the radio message received during the power surge but can only determine that it must be "in some unknown language."

Wildstar and Nova visit the remains of one of the underground cities that Earth used when it had been devastated by Gamilon radiation. Wildstar fears that the new threat could make them necessary again, and knows the the EDF government will not act quickly enough. The encoded message received during the power surge is analysed and determined to be a jammed distress call from outside the solar system -- originating somewhere in the same area as the approaching comet (the issue of it being in some "unknown language" seems to have gone away). But the Earth Defense Committee refuses to take action or to take the possibility of a new threat seriously. Wildstar assembles the old Star Force crew in front of Captain Avatar's memorial statue (Heroes' Hill), and proposes a renegade mission to seek out the new threat.

Against the wishes of Earth government, the old Star Force is reassembled to answer the distress message that Sandor received. Derek Wildstar summons Dr Sane to join them, telling him not to inform Nova. Nova, however, is keen to what is going on and insists she come along. On their way to the Argo's undersea dock site, they pass the Hero's Hill monument once again, where they encounter Mark Venture. Resigned to the apparent fact that Venture is not joining them on their mutinous journey, Wildstar prepares to take the Argo through the water locks. But, just as he gives the orders, Mark Venture arrives on the bridge to take over. "Boy, Venture, you sure had me worried." They take off from the undersea dock against orders, dodging magnetic missiles, and destroying a battle satellite in the process.

Captain Gideon of the Andromeda goes after the Star Force in the Mars-Jupiter asteroid belt, but, like the EDF Commander, decides that their determination and their mission is honourable. He allows them to slip past and reports to the EDC that he merely could not locate the renegades.

The forces from the Comet Empire attack the 11th planet, Brumas, and the Star Force picks up the Space Marines, including their leader, the obnoxious Sgt. Knox. With the enemy threat established, the Earth Defense Commander rescends the warrant for the Star Force, and orders them to seek out information on the threat.

The Star Force is attacked by a fleet of Comet Empire stealth sub-space submarines. Knox begins to resent Wildstar's authority, and unrest grows among the ranks of the Space Marines.

It is discovered that the encoded distress signal originated from a mysterious woman named Treleina of Telezart, a planet on the extreme edge of the galaxy, about 40,000 light years from Earth.

A Comet Empire pilot, Mazor, is captured and interrogated (mild torture). After getting his guard, Dr Sane, drunk on soy bean milk (not a difficult task, considering that it's really sake wine), he escapes. But, turned away by his own fleet, he rams the Star Force in a foolish attempt to regain his honor. Earth learns that, except for the green skin and uncontrollable eye-brows, the Comet Empire race is quite human.

Leader Desslok has been assigned the task of defeating the Star Force. But, Princess Invidia, ever jealous of Desslok, has convinced her father to send General Torbuck to "aid Desslok... and to watch him." Torbuck, feeling over-confident, decides to show Desslok up by defeating the Star Force by himself. He ambushes the Star Force as it passes through a large cloud of meteors. The magnetic fields in the meteor cloud drain the Argo's energy systems, leaving it vulnerable to Torbuck's waiting fleet. Treleina attempts to contact the Star Force to warn them, but Torbuck jams her transmission. However, Desslok cancels out Torbuck's signal. Sandor employs the asteroid ring defense system used on the mission to Iscandar. This time, he has provided the polarizing units with an energy field that absorbs the energy from the incoming fire they deflect, and redirects it back to the Argo in a useable form. With the energy boost, the Star Force manages to fire the Wave Motion Gun at the on-coming antimatter missles, thus, to Desslok's amusement, destroying the missles and Torbuck's fleet. Mark Venture begins to develop a long-distance crush on the mysterious Treleina.

Starflies are cute spaceborn organisms that glow like fireflies. To gain favour with Desslok, Gamilon General Garrot devises a plan to loose a swarm of starflies, infected with a metal-corrosive bacteria, on the Star Force. Thinking them cute, Star Force personnel take the starfly bait, even after the bridge crew observes Gamilon ships on the time radar dumping starflies into space. The starflies get loose, and get into the Argo's systems, resulting in system-wide electrical failure. The Gamilon carrier then moves in to attack. Desslok calls to reveal himself to the Star Force, who are surprised to no end to learn that Desslok is still around. But, Sandor and Roister manage to repair the ship's systems in time to fend off the Gamilon carrier. The starfly swarm has managed to infest the carrier as well, making it defenseless and forcing its retreat.

The Star Force spots a conspicuous-looking hollow asteroid, and decides that it would make for a natural repair dock in which they might repair the damage from the starflies. In reality, it is a Gamilon trap (of course), lined with electromagnetic force-fields. Upon entry, the Argo is stuck. Desslok's fleet moves in to destroy the Star Force with the Desslok Cannon. But Desslok's countdown is critically delayed by a phone call from Princess Invidia, and the Star Force manages to propel itself out of the force-field with the recoil force of the Wave Motion gun -- just in time. Invidia orders Desslok back before he can pursue the Argo. She waits to arrest him on false charges, fearing his designs on the Comet Empire throne. The Star Force arives at Telezart.

The Star Force finally arrives at its destination - the devastated planet Telezart, and are greeted by an apparition of Treleina. They descend to the surface of the planet and fight a land battle with the Comet Empire tanks let by General Scorch. Fearing that Desslok has eyes for the Imperial throne, and that Prince Zordar has taken a liking to him, General Dire and Princess Invidia conspire to turn Prince Zordar against Desslok. Note: This episode formally ties a lot of plot lines together, as it fully reveals the palace conspiracy that is driving the interdynamics of the non-Earther characters. Dire and Invidia's lengthy conspiracy dialogue shows just how sophisticated Star Blazers can be in general.

The ground war is won and Wildstar, Sandor, Knox, and IQ-9 finally go to meet Treleina, under the ruins of her hollow planet. In the Star Force's herbatarium, Nova picks flowers for Derek to give to Treleina. Back on the Comet Empire, Invidia blames the loss of Scorch's forces on Desslok's alledged retreat, in hopes of souring Prince Zordar's respect for him.

Mark Venture flies down to the surface to meet Trelaina. She explains the danger of the Comet Empire and reveals her god-like power which had once destroyed all other life on her planet. She has sworn "never to use that power again to take anyone's life. Never again." Mark begs Treleina to help Earth fight the Comet Empire. But she declares that she must stay behind with her planet even though the Comet Empire is on a collision course with it.

The Star Force prepares to leave Telezart. Mark Venture tries to stay behind. To get him back to the Argo, Treleina agrees to come with the Star Force. But, once Mark is safe onboard, Treleina jumps ship, literally floating back down to Telezart. She leaves a message for Mark explaining her deception and confessing her love for him. She agrees to stand up to the Comet Empire, and stands at Telezart's surface as the Argo pulls away.

The Star Force is nearly out of Telezart's system when the Comet Empire reaches it. Treleina finally makes contact with Prince Zordar, challenging his philosophy of subjugation. Ironically, Zordar's reasons for his campaign do reflect a common state in humanity -- complacancy and laziness. Nevertheless, Treleina rejects his rationale, and turns her entire planet into anti-matter, causing a magnificent explosion into which the Comet Empire plunges at full speed. The Empire eventually emerges from the explosion severely damaged and unable to continue its course to Earth for some time. No trace of Treleina or Telezart is left. Venture is emotionally crushed. Treleina is presumable dead.

Despite its setback, the Comet Empire orders its fleets, under the combined command of General Bleak, to gather for full and immediate attack. Captain Gideon, realizing the urgency of the situation, overrides the Earth Defense Committee and calls in all Earth defense forces to rendezvous at Titan. Meanwhile, Princess Invidia knows that she must have Desslok killed before he can talk to Zordar. She arrives to lead him out of his prison cell whereupon she plans to have him shot for trying to escape. But, the perceptive Desslok has already forseen this, and has made real plans to escape. Leaving the cell, he takes Invidia hostage, and ushers her to Talan's awaiting air car. They dump Invidia at the runway and, with skillful piloting, escape the Comet Empire fortress. Prince Zordar realises he was deceived regarding Desslok, and grants him his flagship in return. The Argo warps to join the Earth fleet.

Nearing the edge of our solar system, the Star Force completes a space warp from which re-materializes right on top of a Comet Empire recon plane (no apparent damage to the Argo). The Star Force passes planet Brumas again on its way back to rejoin the Earth fleet. Despite Wildstar's objections, the Argo's return is delayed while Sgt. Knox is allowed to hold services for the friends he lost on Brumas when it fell to the Comet Empire. While there, he and IQ-9 discover that Brumas has been turned into an enemy ordinance base with lots of missiles. A Comet Empire advance fleet bears down on the Argo. The Star Force destroys the base and the fleet with the Wave Motion Gun.

This is perhaps one of the most favoured episodes amongst Star Blazers fans. Star Force reaches Earth's solar system and joins the EDF fleet. Captain Gideon commissions the Star Force to lead Gideon's carrier fleet in a surprise attack on the Comet Empire's own advance carrier fleet near Saturn. Thus, this episode gets its title. Sandor and IQ-9 takes a short recon flight to Phoebus, Saturn's 10th moon, to locate the enemy's fleet. The fleet is ambushed and defeated by an Earth carrier fleet led by the Argo. This episode features a really swinging version of the Yamato main theme (often called the "Disco Yamato Theme") played as the EDF squadrons launch.

The Comet Empire main fleet makes their final stand at Saturn. General Bleak's Magna Flame gun manages to destroy a sizeable chunk of the Earth fleet. Earth's remaining forces retreat to Saturn's ice rings wherein they ambush the Comet Empire forces. The Argo, late to join Captain Gideon's fleet, is not able to participate the the main battle but sends fighter squadrons. After defeating the Comet Empire fleet, the combined force of all the Wave-Motion Guns in Earth's fleet succeeds in disabling the plasma vortex that enshrouds the Comet Empire fortress. But, the secondary plasma shield that covers the upper half of the fortress remains operational, and the Comet Empire's main belt guns manage to wipe out the entire EDF fleet. Captain Gideon and his Andromeda crash headlong into the Comet's plasma vortex but not before radioing a message to the Star Force that they should attack from the bottom. Note: This episode features the really grooving version of the Comet Empire theme, as Bleak's fleet plunges into the heart of the Earth Defense forces.

The Star Force retreats to Ganymede for repairs, and the Comet Empire rejects Earth's attempt at negotiation by blasting the moon into a molten state. Note: Just how much of the moon is blasted is uncertain. It is still in the sky later during the movie, Be Forever Yamato.

The Star Force leaves Ganymede to defend Earth, but is again attacked by Desslok. Almost regretfully, Derek Wildstar gives the order to fire the Wave Motion Gun at Desslok's fleet. But, the clever Gamilon uses his SMITE teleportation device to position space mines around the Argo's bow... threatening certain detonation if the Wave Gun is fired. Just as Desslok fires his Desslok Cannon at the Argo, the Star Force performs a small space warp, and ends up ramming into Desslok's own ship -- in perfect symmetry of the actions of Desslok in the last episode of TV Season 1. The Star Force invades Desslok's ship for a hand-to-hand fight. During the boarding, Nova and Dr Sane watch helplessly as Venture is blown into space by an explosion. Both ships are rendered inoperable, and the ever-practical General Talan convinces Desslok that he has effectively won, and should abandon the ship. Reluctantly, the Gamilon Leader agrees. Turning to leave, Desslok finds Windstar facing him on his bridge. The Comet Empire lands in the Great Eastern Sea (off the coast of Japan) on Earth.

Wildstar, badly injured, reaches Desslok's command bridge. At the moment of the inevitable pistol duel, Derek faints and Nova rushes in to catch him. Seeing Derek and Nova's devotion to Earth and themselves, Desslok sees his own nobility. He laments the futility of his battle and vows never to fight (Earth) again. Echoing the advice of Captain Gideon, Desslok tells Nova the secret of how to defeat the Comet Empire from it's bottom side... and simply leaves. We learn that Treleina still lives, and rescues Venture floating dead in space. The Star Force pulls free of the wreck of Desslok's flagship and prepares what meager assortment of weaponry it has left for the final, undersea assault on the Comet Empire.

Just as Earth officials are leaving to sign the surrender agreement, the Star Force begins its surprise undersea torpedo attack. They roust the fortress aloft. After a frantic fighter battle above Earth, in which we later learn that pilot Hardy has died, a desparate invasion task force -- Wildstar, Sandor, Conroy, Knox, et al. -- penetrates the Comet Empire through openings in the bottom side. Sandor's bionic leg is blown off the ensuing shoot-out. Sgt. Knox manages to reach the Comet Empire energy centre. He tells Wildstar and Sandor to return to the Argo, and that he will follow. Once they are outside the Comet Empire, Knox manually sets off the small hydrogen bombs that destroy the energy center (and actually Knox too, though English dialogue denies this). The Star Force launches one, final, all-out barrage against the powerless Gatlantis fortress. The rubble churns into fire. When victory is thought won, a deadly black ship, Zordar's dreadnaught, rises from the ruins. Zordar threatens to leave Invidia and General Dire behind in the exploding fortress for all their meddling (actually, in the Japanese version, he does!).