Mission: Missing Supplies
At the marker you talk to George Washington, who though he has no world of Lee tells you that some of the supply caravans have gone missing. He mentions a traitor named Benjamin Church, who George explains sent letters to the loyalists that detailed the troop movements. Connor vows to find Church for Washington, and Washington mentions reports of trouble along the southern roads, and suggests that you start the search there.
After the CS ends the game adds entries to the Animus Database for the Continental Army, Valley Forge, and an update to the Benjamin Church file, all of which are worth reading.
When you reach the abandoned church at the marker you get a CS in which you reunite with your father – and the conversation is an interesting one. He tells you that the Templar are not aligned with the British, but serve their own aims. He makes a compelling set of arguments, and then he offers you a deal... Your dear old Dad proposes a truce and cooperation – really? Really?!
Outside is a clue to be examined that reveals the contents of the crates - doing this narrows the search area which is marked on the map. Note that there may be a patrol of British soldiers nearby and you should avoid dealing with them if you can, since you know, that is really not the point of this.
Ahead on the road you find cart tracks as a clue, then the cart and the cart minder, who runs off when you ask if he serves Church. You have 30 seconds to chase him down and capture him to complete the optional objective - be sure to change your active weapon to Hand and then tackle him. You start to interrogate him but your father blows his head off (?!). Clearly there is something Da has not told us and does not want us to know.
A new marker appears that leads to the cart caravan and once you get close you are supposed to follow it. The optional objective for this is to NOT hide in the hay wagon - instead use the trees to keep pace with and eavesdrop on the conversation.
Helping General Washington deal with a Traitor
Eventually you will arrive at the point where you have to leave the trees and trail the two men on the ground. Once you hear enough of the conversation you will find yourself in the Hay Wagon you were not supposed to use for the optional objective. A new optional objective has been added – kill the three guards without being detected. You can kill the first one as a stealth kill from the wagon, and another by killing from hiding in the brush. The third you kill inside the ruined building ahead.
Continue to follow the pair until it triggers a CS in which your Dad is captured by the hooligans – make sure you arm a weapon (you may still be using hands) and then attack to save your father – who then tells you to deal with the mercenaries telling you to meet him in New York City later.
The fight you are about to have is badly griefed in that your ability to defend yourself is hampered by a tighter than usual timer on using defensive moves. You will find that most of the guys with muskets must be disarmed BEFORE you can kill them. Basically this is one of those instances where you are rewarded for going berserk and killing quickly...
An alternate tactic is to simply shoot most of them – if you have been paying attention to the crafting system you will likely have upgraded your ammunition capacity and crafted the double-holster and, if you bought the two-shot pistol that gives you four shots before you need to reload – so kill the ones you would ordinarily need to disarm first by shooting them, slice the throats of the ones you can, then run around and reload, then rinse and repeat until done!
After that all you need to do is leave the marked area and you are done with this mission. A marker appears on the New York City fast-travel point since you need to meet Haytham there. Before you do that though there are some other things we need to do first.
Achilles Conversation Icon
Check the map and you will see a nearby conversation icon - tag it then go there and you will talk to I think Lafayette? Have the conversation with him and then head to New York City.
On the trail of Church in New York City
Mission: Father and Son
Head to the Main Mission Marker on the map and you find some guys sitting on a bench at the open market – when you start he mission your father shows up and greets you, then tells you where Church is holed up. Connor tells his father that he wants the supplies returned and Haytham agrees to that, then tells Connor to follow him. Well? Follow him!
He leads Connor on a path over the roofs and then you get a CS in which Connor asks the question we have all been wanting to ask. His father tells him what the Templar philosophy is, and hints at his Assassin origins and the reason why he changed sides. After the conversation concludes, the rooftop journey continues until you climb down a ladder and get another CS.
Your father indicates that you cannot come with him as the guards will react to you. Connor tells him that he will find a guard to steal his uniform, and his Da says he will wait. Your main objective is to disguise yourself as one of Church's men – the optional objective is to not be detected while you steal a mercenary outfit... The counter indicates you are only supposed to kill one person.
The target Mercenary is marked on your map – unfortunately in the process of getting to him you will likely be harassed by beggar children and there is a patrolling pack of British Redcoats who will move through the area. There is a hay wagon but you cannot actually use that to kill the Mercenary – likely since you need to be able to change into his uniform and you cannot do that in the hay wagon.
You can use the hay wagon for concealment while waiting to time taking down the Mercenary but be aware that when the British patrol comes by the officer will search the wagon with his sword and reveal you if you are in it, thus causing the optional objective to fail.
There are two ways you can do this - either get lucky on the timing and take him down in the alley and not get seen, or you can use the hay wagon but jump out the opposite side when the officer searches it so you are not discovered, wait for the patrol to leave, and then take the Mercenary down in the alley at your convenience. Another tactic is to sit on the bench and wait for the patrol to leave, then assassinate the Mercenary and loot him to get the clothes and trigger the CS of you and your Da entering the warehouse in mufti!
That completes the mission, and you should get full Synchronization if you hit all the high marks - you did, right? Of course you did!
Seeking out Church in the Brewery
Mission: The Foam and the Flames
Now you are inside and you are supposed to follow your father to confront Church – the basic objectives besides that are to escape from the brewery in order to resume pursuing Church, who as you may have guessed runs. They always run... Why do they always run?
During the CS your father learns that Lee did some things that he was not supposed to – then you go in to confront Church but things go pear-shaped and you end up having to battle a group along side your father. The remaining agent tells you what you needed to know, and then your father kills him!
A group of Mercenaries fire into the brewery and blow up some barrels, setting the place on fire, and you need to escape, but the optional objective for this mission is to escape while taking NO fire damage! That can be a bit tricky but if you follow the markers you will manage it. When you get to the end of the line you distract some Mercenaries who have cornered Haytham and then you get an amusing CS.
You know the odd thing about this is that Connor is working with his father and what seems worse to me is the fact that he is going to reveal the Aquila to him. Don't forget his father is a Templar!
As long as you have been following the guide and you stayed on top of the side-missions there is no reason not to go ahead and begin the next mission.
Final resolution with Church and the Supplies
Mission: A Bitter End
You row out to the ship with your Da and then you are in the Caribbean and at a familiar location - this was the hiding place we had to thread to go after a different ship. The optional objective here is to limit environmental damage to 20% so try not to hit the rocks, and thread your way through then head to the search area and you find the Welcome abandoned in the cove.
Just as you examine the abandoned ship a smaller boat shoots at you and you give chase. The optional objectives here are to stay within 500m of the smaller boat and you should be able to do that by rapidly managing your sails – using full sail when the “rogue winds” are not blowing and when you do not need to turn sharply to maintain speed, but reducing sail for the winds and turning. Once you reach the pre-set point you encounter the other boats mates including a large Man of War and you need to then cripple the larger boat using Chain Shot, and take out its out-runners. Once all of the gunboats are destroyed (use your Swivel Guns) you can then approach and board the disabled enemy.
Boarding this time around does not work the way it did in the previous Naval Missions, as in those the process was automatic when you sailed close but this time your father does it for you.
There is a ****-move on this mission – the optional objective is to obtain a three-kill-streak – the ****-move part is that they make it very difficult to do direct kill initiations with the regular soldiers or sailors, so it works best if you start with an officer and then kill two of the crew to get the optional objective done, and then do the other officers.
You get a CS and then you are below decks, looking for Church. You find him being beaten to death by your dear old Da – and when you question him he tells you where to head in, so you kill him. That initiates an Animus interrogation during which you get the information you are seeking. Church has his say, as is the tradition with this event, and then you have a little more to think about.
That completes the mission, and gains you full Synchronization as well as unlocks the Achievement “Two if by Sea” (20G)
for completing Sequence 09.
The end of this Sequence includes another monologue by Connor who sums up his emotions and the thoughts that he has been having.
You end up back at the Homestead where you get a CS of a conversation with Achilles, during which you man-up and apologize, but it seems that Achilles agreed with part of what you said. Achilles guesses that you have met your father, and Achilles seems resigned to your new path.
Head to the Frontier and look at the map to see that the Mission Marker is located at a spot on the far-left-side of the map. Head there (if you have already flagged the fast-travel spots for the Stores you can use the nearby one). When you arrive you will find yourself in Valley Forge and as you get closer to the marker you will see military fortifications – which should clue you in on what is coming :)