When the book opens, the war is already well underway. We meet Morgan Clark, who is ranking member of the Earth Alliance Senate Armed Services Committee and member of the Senate Intelligence Committee. He is a balding man in his 40s. He is not insane (that comes much later), but he is driven by perhaps equal parts desire for power, and paranoia: both traits that helped him rise to the high government position he now finds himself in.
He is paranoid about telepaths (as is standard)
He is paranoid about traitors within EarthForce (confirmed by Franklin's actions, and also apparently confirmed by Sinclair's survival)
He is paranoid about traitors on Mars (the Free Mars movement begins during the war, and Mars also refuses to fight - so they're all turncoat cowardly traitors to him)
He is paranoid about alien betrayal (the Centauri and Narn aren't apparently lifting a finger to help Earth, despite long-standing diplomatic and economic ties with both races)
Above all else, however, he is traumatized by the war (as is most of Earth), and deeply paranoid about the Minbari. He fears Bester would work with the Minbari (he doesn't), he sees Franklin as a Minbari sympathizer, if not agent, he sees Sinclair as definitely Minbari agent (though the Minbari apparently wiped his mind so he wouldn't know it - unless Sinclair is lying about that, too), he sees the Babylon Project as another attempt by the Minbari to spy on and ultimately conquer Earth somehow, and on top of all that, he believes President Santiago himself to be working for the Minbari.
"Elected as EA President in 2253, Santiago was a great supporter of the Babylon Project, an initiative inherited from his predecessor Elizabeth Levy, persevering despite the first four stations being destroyed or disappearing without a trace. When B5 finally went on line, Santiago allowed the Minbari to choose Jeffrey Sinclair as the station's commander, though left orders in place that if anything happened to Sinclair, Captain John Sheridan would take his place. Due to the support of the Minbari, Santiago gave Sinclair complete authority over all matters on the station."
The station is supposed to be under Earth military control. But then the president of Earth lets the Minbari pick the EarthForce commander to lead it, and they pick the pilot who is a known agent of the Minbari, and the president is like "yeah, sure, sounds fine to me"?
The Minbari didn't just pick their own people - they have a veto over EarthForce now? They rejected every candidate until they got all the way down the list to Sinclair, and Earth didn't tell them to shove it? Santiago said OK?!
Ever since the end of the war, Clark had been working with IPX and others he trusts to find a rumored alien race that is much more powerful than the Minbari, who could protect Earth from them. (He honestly cannot imagine any race worse than the Minbari, who killed hundreds of thousands, and almost destroyed every single human alive, but then decided to let them live and psychologically torture them instead.)
He keeps working with these trusted associates to find the Shadows under Santiago's nose, even as VP, and then, after they (Santiago and Clark) win reelection, he works with the Shadows to assassinate Santiago and take over.
Not just because he wants power - which he does, because he believes that he personally needs to be in charge in order to protect Earth from the Minbari, and their spies and agents. He assassinates Santiago because he believes Santiago is working with the Minbari and is a traitor to Earth. He sees the whole Babylon Project as corrupt and dangerous. Sinclair is running it, Franklin is the chief medical officer even though he's wanted on Earth for treason, the Centauri and Narn ambassadors are the same two who (as he sees it) wouldn't help Earth when Earth was invaded, the place is crawling with Minbari, and so on.
I think it's also interesting if the Shadows (through the agents they are using in this time period - this is before Morden) help plant the idea in his head that Santiago isn't just a fool, but a dangerous traitor. They tell him everything he wants to hear.
