A mysterious mobile suit infiltrates the space colony known as Gryps, headquarters of the dreaded Titans. Its pilot is Char Aznable, the infamous Red Comet, who now fights for the rebel AEUG group under the alias Quattro Bajeena. After confirming that the Titans are developing a new Gundam mobile suit, Char rejoins his teammates at the civilian colony Green Noa 1, where more of the new Gundam...

Char's team breaks into Green Noa 1 and begins a running battle with Federation Forces mobile suits. During the confusion, a young civilian named Kamille Bidan escapes from the Titans' custody and commandeers one of the new Gundam Mark II units. Out of hatred for the Titans, Kamille helps the AEUG capture a second Gundam and then joins the rebels in their escape from Green Noa 1.

Char and Kamille return to the AEUG flagship Argama with the captured Gundams. Meanwhile, the Titans dispatch the warship Alexandria, as well as reinforcements from the regular Federation Forces, to pursue the rebels. Titan pilot Emma Sheen is sent to the Argama to deliver a message from her commander Bask Om, but she is as shocked as the AEUG when the nature of Bask's ultimatum is revealed.

After Kamille fails to rescue his mother from the Titans, the AEUG are forced to hand him and the captured Gundams over to the enemy. But Emma, horrified by the actions of her commanders, decides to defect to the AEUG. With Kamille, his father, and all three Gundams in tow, she makes a desperate attempt to escape to the Argama.

With all three Gundams now in their hands, the AEUG begin breaking the machines down for research and spare parts. In the middle of this, Kamille's father steals one of the AEUG's own mobile suits and sets off for the Alexandria, hoping to regain the favor of the Titans' leaders. The AEUG and Titan ships begin a pitched battle as Kamille and his father confront one another.

The Argama descends into Earth orbit to send AEUG agent Reccoa Londe on a reconnaissance mission to the planet's surface. To distract the Titans, Char leads a diversionary attack on a solar power satellite. Meanwhile, after being repeatedly humiliated in battle with Kamille, the Titan pilot Jerid Messa seeks guidance from Federation Forces ace Lila Milla Rira.