For the Republic, Part 2: There is a way to oust McNamara and have a peaceful outcome. However, once you talk to Hardin and begin the process of overthrowing McNamara, you just simply don't go back to the Brotherhood of Steel bunker until you've talked to Moore about the Brotherhood. Hardin doesn't "officially" become Elder until you return to the bunker.
When Veronica Santangelo is in your party, Hardin will tell Veronica that "it's dangerous outside" and that he "hopes she's been practicing her drills."
Veronica mentions that Hardin taught her how to box when all the other Paladins refused.
During her quest, I Could Make You Care, Veronica describes Hardin as an unyielding man who would charge her with sedition if she continued to push her ideas of getting the Brotherhood to change its course.
If Hardin is to become Elder, the optional objectives of the quest Still in the Dark must be completed.
"Elijah was a strange one. His even becoming Elder was highly questionable, seeing as how he was a Scribe. Typically, only Paladins are eligible. But an exception was made in his case, on account of him being a genius. Unfortunately, whatever scientific acumen he had didn't extend to tactics. Trying to defend HELIOS was a blunder of the worst kind, and many brothers lost their lives because of it. Many of the senior paladins, myself included, advised him to fight a retreating action, but he refused to budge. Said he almost "had it working". We never did find out exactly what he was talking about. When the perimeter was finally overrun, the Elder had simply vanished."
"As you may have already heard, this entire base is under a state of lockdown. No one goes out except small patrols at night. Most of the chapter has been Morale has plummeted as time has gone by, and many of our current paladins haven't even seen combat outside of training simulations. And all because of the Elder's explicit order that no one be allowed in or out. The only way things will change is if a new Elder is installed."
"Yes, I know the loss of the patrols has weighed heavily on his mind for some time. He took it very personally when they first went missing. That was when I first began to seriously question his ability to lead us. A commander has to be able to deal with the potential loss of his men. It's strange that he would ask you to find mission discs on them, however. The missing paladins were all on standard patrols, which don't need them. Only Brothers sent on special assignments are given mission discs. If you should find any on the lost patrols, let me know."
"Back when we were stationed at HELIOS, our scouts reported that a group was establishing itself in the area as a distributor of Pre-War weapons. Our Elder at the time, Elijah, was too concerned with getting HELIOS running and fending off the NCR, so he ordered us to leave them alone. It's time that we correct that oversight, and show this region that the Brotherhood is still a force to be reckoned with. I want you to visit these weapons dealers, this Van Graff family, and make an example of them. Leave no one alive."