I place the good of the Vault above everything, even my own paternal feelings. We must not allow sentiment to cloud our judgment! But I admire your protective instincts. Very well. I give you my word that Amata will not suffer further because of your actions. Now then. If you really care about Amata, you will see how dangerous your father's actions were. Hand over your weapons, and put an end to this dangerous situation. There's no need to join your father as a traitor to the Vault.
Growing up in Vault 101 during a time when the vault dwellers ventured freely into the outside world, Alphonse's parents believed the vault should have no contact with the dangers out there. As he got older, Alphonse knew he had to correct the gross lapses in security. He got his chance when the preceding Overseer - a strong proponent of outside contact - disappeared one day while out in the wasteland. Many suspected foul play, but Alphonse Almodovar offered the vault dwellers new leadership, and they had little choice but to accept. 
In late 2258 or early 2259, Overseer Almodovar accepts James and his child into the vault, and James is assigned to be the new vault physician.
In 2260, Alphonse is widowed and left a single father when his wife dies from an unknown disease.
Unlike his predecessor, Alphonse Almodovar adopts a policy of isolationism for Vault 101: "No one ever enters. No one ever leaves.", and also "Everyone was born here and everyone will die here."
Almodovar is a widower with one child named Amata. He is very heartless to almost all of the vault residents, including the Lone Wanderer and father James.
The dossier on Amata, located in the Overseer's terminal, reveals that he feels conflicted between his role as father and his role as overseer, attempting to find a balance between the duties that come with both. Despite his harsh and heartless interaction with all those who live in the vault, including Amata at times, it appears he desperately wants to connect with his daughter. He states that no matter what he tries Amata just seems to see him as "The Overseer".
Escape!: When James escapes, Almodovar thinks that the Lone Wanderer had something to do with it, so he sends his security officers after them. He orders the death of Jonas after James' escape and interrogates his own daughter. Depending on whether or not he is killed, Amata will react differently to the situation.
There is a photograph of Alphonse and his daughter Amata in her room.
During Trouble on the Homefront his computer terminal reveals that, after leaving, the Enclave contacted the Vault in an attempt to gain access, but he denied them entry as he would not trust the lives of the Vault inhabitants to outsiders.
He will call characters "young men" even if playing a female during dialog in Trouble on the Homefront. He is also always identified as "The Overseer", even if he relinquishes the position to Amata. These are some of the many oversights in the interactions with Alphonse.
At the 10th birthday before going to the reactor level, following the Overseer as he goes past the reactor, up some stairs and engages in a dialog with Officer John Kendall, he lets out that the only reason he came [to the party] is because Amata's friends with the brat (the Lone Wanderer).
If fought during the quest Escape!, he can sometimes say "The Overseer will hear about this!" even though he is the Overseer.
Moreover, if he is provoked him attacking and if not killed, he will relentlessly follow (even when talking with Amata) until Vault 101 is left.
If he is not fought and the agreement is to turn oneself in, he will confiscate the weapons and immediately use them himself.
"I place the good of the Vault above everything, even my own paternal feelings. We must not allow sentiment to cloud our judgment! But I admire your protective instincts. Very well. I give you my word that Amata will not suffer further because of your actions. Now then. If you really care about Amata, you will see how dangerous your father's actions were. Hand over your weapons, and put an end to this dangerous situation. There's no need to join your father as a traitor to the Vault."
"And you expect me to believe that the only way to do that is to let them travel out in the Wastes and mingle with those savages? I suppose it would allow them to stay alive, and we could still keep the Vault as our safe haven. But it'd require a new type of leader. And I know only one person with the proper attitude to do that. I'll inform my daughter Amata that she is the new Overseer, effective immediately."
"Really? And here I had expected you to be full of bullets and bravado, but short on brains. Perhaps you've grown up since you left our Vault. I regret the unfortunate events of that night, but I'm afraid that once your father left us, they were unavoidable. The sad truth is that his actions presented a real and direct threat to the future success of our Vault. And so, regrettably, they had to be opposed."
"And what makes you so certain about that? I can't imagine you're still so naive after spending time in that hell outside. None of them know what the outside is like, and most of them would die out there. Then the rest of us inside would eventually die out, too. I won't risk all of our lives just for few people's passing fancy of taking a Wasteland vacation. I hope you can understand that."