Okay, here is what I made out of your logs...hope it works out. I think it's a pretty good summary.
Zion Mission 11.2.5: 101
Zion continues it's search for the BIP and preventing bluepills from being massacred by Wright. A contact tips you off about where the BIP is and the contact is the Morpheus simulacrum. Apparently the sim and the BIP happen to be working together and the phone trace by Morpheus leads to an apartment in Eshean. The BIP leaves you a message on the computer in the apartment... "Knock, Knock." Is this who I think it is?
Machine Mission 11.2.5: Antigenic Sin
The Machines and Cryptos continue to rid the Matrix of Override infestation and Cryptos has been working on some Anti-override Prototypes. He decided to make a trade with the Machines only if he got some info from the Machines about some things. They didn't last long but they did protect you from override activity. You later find out that the Overrides were put in place in the Matrix before the war and the contact of humans. Wright is still chasing the BIP through the Matrix.
Merovingian Mission 11.2.5: The Apartment
Persephone arranged a meeting with you and she seems to be a little ill...she turned goth and emo! Anyways, sad about the bluepill's death she wanted to talk to Wright. Persephone wants Wright to stop this madness but Wright believes that she is fighting a war and will stop when the Matrix is run by those who power it. The BIP leaves the message "Wake Up" on the Merv's network.