As Capt. John Sheridan's forces approach Earth, the fighting grows more fierce. Out gunned and unable to flee, President Clark's remaining ships still refuse to surrender.Meanwhile, Dr. Stephen Franklin and Lyta Alexander find themselves on Mars again with their disturbing cargo. Michael Garibaldi matter of factly informs Edgars that John Sheridan's trap has been baited with his father. Pleased, Edgars again promises Garibaldi the elusive reward of the whole truth. "I think the last guy got thirty pieces of silver for the same job," Garibaldi remarks with distaste as he leaves.
Sheridan orders the opposing vessels to stand down again. One captain finally breaks silence saying that Sheridan is only going to execute them if they surrender. Sheridan's new ally MacDougan convinces the young captain that its safe to stand down just as a new ship jumps into the melee. To Sheridan's relief it's his old ship, the Agamemnon, come to join his fleet.
Number One is livid to discover that Franklin has brought a "teep" (telepath) into her facility without even thinking of consulting her. The dozens of frozen telepaths he brings are equally unwelcome.
Sheridan and the Agamemnon's crew share a fond reunion when he goes on board. He's still there when Garibaldi's transmission catches up with him. In it Garibaldi explains that Clark's people have captured Sheridan's dad, and says he has a rescue plan which requires his presence. Against everyone's advice Sheridan decides to go to Mars alone, and the Agamemnon agrees to transport him there.
The hostility towards Lyta is not limited to Number One. Franklin is baffled, until Lyta explains the Bloodhound program. Anyone suspected of being in the Resistance is simply picked up and scanned, without any due process of law. Quietly Lyta begins to explain the other things Psi Cops have done. One serial killer of telepaths now lives in an institution, screaming all the time at the "things [we] planted in his mind." When that happened she left Psi Cops for commercial work, but from then she became afraid of what telepaths are capable of. "Someday there's going to be a war between telepaths and mundanes, Stephen," she predicts direly. Within the series the term "mundane" is used by telepaths (usually derogatorily) when referring to normal humans without their abilities, much like the use of "teeps" toward telepaths.
Sheriden pilots a fighter down to the surface of Mars, where Garibaldi is waiting in a bar. Shortly after as the Captain sits and begins their conversation, Garibaldi slaps a tranquilizer patch on his hand. Furiously Sheridan stands and attempts to escape, but the men who have come for him are too many and too strong. Garibaldi just sits in his place and watches impassively as his former friend and CO gets beaten and taken into custody. ISN's gloating over the capture begins almost immediately. Ivanova and Marcus Cole watch in stunned silence.
Garibaldi returns to his boss, furiously demanding to be finally told the truth. Edgars and Wade reveal that they have genetically engineered a virus that attacks only telepaths. They have also developed an "antidote" that needs to be administered to infected telepaths every two weeks. Turning telepaths into a virtual slave race is the only way they see to counter the threat of the "death of human liberty and human thought." As a side-effect, by removing Clark's power base in the Psi Corps, they will be free to overturn his government easily. Garibaldi affirms that he is still on board and Edgars informs him that now that Clark is distracted by the capture of Sheridan, he can begin the process of releasing the virus. "The telepath prob--" he utters and stops. Hearing the holocaustic parallel in his own words, he continues in a broken voice, "The telepath problem...will finally be over." Unbeknownst to them all, a horrified Lise has heard everything from her hiding place behind a column.
When they have left the room Garibaldi sits quietly and pops a cap off his tooth revealing a minuscule transmitter. Lise finds him later waiting stony faced in a tube, where she begs him to help stop her husband. With eerily muted urgency Garibaldi only tells her to go home. Moments later a new passenger joins him and the car leaves the station. Without hesitation, Bester enters into Garibaldi's mind and extracts Edgars' nefarious plan. Even the normally imperturbable Psi Cop is stunned by the extent of this "final solution." Having finished what he came for, Bester muses about what to do with Garibaldi next. "I can feel you, you know...the real you, beating at the inside of your skull, screaming to get out." Should he let Garibaldi free? Should he keep him penned up forever? He explains to Garbaldi what happened when he was captured by the Shadows.
Bester got control of Garibaldi during the Shadows' attempt to "adjust" him and managed to handle the procedure on his own terms. That way he could thwart his enemies the Shadows (the virus of Edgars' was likely Shadow technology after all), take revenge on the officers of Babylon 5, and use Garibaldi as a weapon against his other enemies, all in one move. Accentuating his naturally rebellious and suspicious instincts, Bester states, would turn Garibaldi into the perfect tool for digging to the possible anti-telepath conspiracies. The odd messages Garibaldi received from time to time tuned his conditioning until his real personality was completely buried under the new one. And now Bester wonders what to do. Toying for an instant with a gun in Garibaldi's face, Bester comments that now that Garibaldi's friends know he betrayed Sheridan, he "can't go home again." Deciding to let the real Garibaldi free, Bester exits the car and the train leaves the station. Garibaldi sits impassively on the bench. A flash of reality slams his mind. He shakes his head. Then another. And then again. He screams in rage and whacks his head into the wall of the train.
When Marcus informs Ivanova that Garibaldi has attempted to contact them, she orders that if he shows up on the station he be shot on sight. In the interim, with Sheridan captured and the fleet in limbo, she vows to finish the job her Captain began. Garibaldi frantically searches Edgars' home for Lise but only finds Edgars dead, the virus removed and Wade, Edgar'a assistant, mortally injured on the floor. Wade manages to whisper that Lise hadn't been there when they were attacked.
The ISN anchor reports the assassination of William Edgars apparently by Free Mars terrorists. She also proudly congratulates former Chief Warrant Officer Michael Garibaldi for rescuing the renegade EarthForce Captain John Sheridan. While Sheridan continues to be pummeled by his captors, she reports that now that he has been freed of alien influences, being well cared for, and has expressed regret for his actions against his home world.