After Sequence 4, Assassin’s Creed 3 actually begins; get to the checkpoint on your map to start the first mission in this sequence.
Assassin’s Creed 3 – Sequence 5 100% Sync
Mission 1: A Boorish Man
You meet with Achilles, after failing to get into his house several times camp in his barn to avoid the rain. Before long, you’ll have to fight off a group of bandits on his lawn, after which he’ll deign to speak to you.
Simple stuff, really. Kill everyone, then head to Achilles’ house for a conversation. Don’t lose too much health in the fight, or you’ll fail the 100% sync requirement.
Mission 2: Trip to Boston
Now you need to go to Boston. Explore the city as much as you wish, but when you’re ready to progress run the errands that Achilles wants you to then go talk to him by the wagon. Follow the man whom he points you to and kills him when prompted.
Now you need to escape so run along the rooftops until you see a hay pile below you to hide in. Birds congregating around the edge of a building rooftop usually denote locations you can jump from into the hay. Make sure you get away within 80 seconds for 100% synchronization.
Mission 3: Boston’s Most Wanted
An associate of Achilles will instruct you on how to reduce your (now) high levels of notoriety. You can track the guards on your mini map, and as long as you stay on the ground, you won’t have to worry about the faded dots that indicate rooftop snipers.
After ripping down two of the posters that are highlighted, go talk to Sam Adams. His friend will help reduce the last level of notoriety off you. The optional objective for 100% sync rate is that you must not get level three notoriety.
Mission 4: Lying Low
This mission consists mainly of a trip through the sewers. You will have to light candles as you progress and observe as the rats move under the walls to find the correct path, then lock pick the door to move on.
Bribe the printer to alter his propaganda then take a boat back to the Davenport Homestead to move on to the next mission.
Mission 5: River Rescue
You need to rescue Terry before he reaches the waterfall, without touching the water if you want full synchronization. Take the path of logs that are jutting out of the river itself.
It’s a fairly straightforward route, and once you have reached the branches at the end of the path; you will be able to jump for him without getting wet.
Afterwards, walk back around the lake to the East to where the fast travel location is. Find Achilles standing out by a shed.
Talk to him to meet Robert Faulkner, the first mate of the Aquila. The Aquila is the broken ship right outside that can be repaired again. After talking with him, return to the manor above the lake. Follow the on-screen steps for learning about the Ledger.
Mission 6: The Hard Way
Fast forward six months and the Aquila is fixed and ready to go. Head down to talk to Robert in order to set sail in your new ship. After the cut scene head for the steering wheel where Robert teaches you to be a naval officer.
Eventually, you’ll get to use the ship in sea combat but there isn’t anything really complicated here, just follow the on screen instructions, and you’ll do fine. Remember to use the swivel guns on the smaller ships, and the cannons only once the big ships attack.