You'll appear in Kuro's room and receive Memory: Divine Dragon and the Divine Dragon's Tears. Talk to Emma to receive the Secret Passage Key. One of her dialogue options is "Isshin's parting words?" If you have unlocked the final skill of any skill tree, Emma will give you the Mushin Esoteric Text. If you haven't, you can do so later, then come back and talk with her before ending the playthrough. It's hard to gauge when you will be able to, but when you do unlock the final single skill in any of the skill trees, a trophy will unlock:
Commune/rest at the idol and notice that the idols in the castle are grayed out again. Enhance attack power with Memory: Divine Dragon to permanently increase your attack power (from 10 to 11), then head out the open window. Follow the roof around to the right and grapple into the open window a couple of levels lower in the back of the building.
Commune at the idol, then circle around to the right so you can kill the Lone Shadow samurai from behind (he gives 1052 exp!). You could farm this guy for exp and sen if you wanted to by stealth killing him, then running to rest at the idol and repeating.
Run through the large room, past another Lone Shadow samurai, and make your way up the stairs to the Ashina Dojo idol. Commune/rest, then go back downstairs and around to the left to the weak wall that can be broken. Smash through it and continue forward to see an enemy kneeling in front of you. If you approach slowly you can eavesdrop but you can't sneak up for a stealth deathblow without him sensing you. You can run away so he loses aggro, then sneak up for the first deathblow, though.
This is Ashina Elite - Ujinari Mizou (VIDEO), the strongest Ashina Elite. Like the others, he attacks with his sword from a sheathed position incredibly fast and deals huge damage- both to health and to posture- if not deflected precisely. The best way to beat him is through deflection and it's completely possible normally, but using the Loaded Umbrella makes it a lot easier. Stand face-to-face at the ready and when you see him go for his sword (indicated by a flash of light by his hand), immediately press 
to use the Loaded Umbrella and it should deflect his attacks and deal a lot of posture damage to him. Repeat this until you can perform a deathblow, then repeat until you can perform another if necessary, after which you'll receive a Prayer Bead (38/40).
Travel to Kuro's Room and head out the open window again. Look down to the area below where numerous enemies are fighting each other.
Make your way down there and then go to the Ashina Castle idol at the base of the steps- you can drop down, grapple to land safely, and run along the rooftops to the end. Commune and rest, then from the idol look at the steps and go to the left. Run past the two fighting enemies and into a building, then drop down and get to the Ashina Reservoir idol. Commune, then look ahead to see two enemies at the far side of the area. Inch close enough to Eavesdrop.
Then inch closer and the first enemy should start moving towards you. Stand on the ledge at the top of the steps and when he gets close enough, jump over him and do a deathblow from behind, then activate Puppeteer Ninjutsu. The other enemy, Seven Spears Ashina – Shume Masaji Oniwa (VIDEO), will notice the commotion and come your way. Try to stand back and watch them fight until the friendly enemy is killed, after which you need to finish off Shume to receive a Prayer Bead (39/40). He is essentially a stronger version of the Seven Spears warrior from this same area but much earlier- deflect his attacks, jump over his perilous sweep, and counter his perilous thrust until you can deal both deathblows.
Another option would be to run behind to the seated, nonhostile enemy along the wall, which will stir up Shume and his friend. Backstab the seated enemy, then use Bloodsmoke Ninjutsu so you can stealth deathblow the samurai enemy, leaving Shume by himself (VIDEO).
Once you're done here, travel back to the Ashina Castle idol and go back to the stairs. Grapple up to a roof on the right and make your way up to the top of the rooftops. Look in the distance to see a kite and head towards it.
Once you get to the closest rooftop, you can grapple to it to launch across and land in a lower area where you'll see a bridge in the distance. This area should look familiar- the bridge used to be broken and now leads to the Ashina Outskirts. Run across the bridge and past the fighting enemies (including a mini-boss) and into the building ahead. Continue forward into the area where you fought the Chained Ogre very early on and grapple up to a platform ahead to reach a Sculptor's Idol. Grapple to a nearby tower to stealth kill an enemy, then drop down and stealth-kill a second. Move forward to take out a third, then there will be two more marching up the steps. Kill both (will likely require Bloodsmoke Ninjutsu) and then head back into the building to face Shigekichi of the Red Guard (VIDEO), who is below the hole in the building. Start by sneaking out onto the ledge and killing the alarm enemy to the left, then go back inside and around to the open doorway. Watch for the patrolling enemy to approach this door, then kill him from behind when he turns around (GIF). Get back onto the ledge above Shigekichi and drop onto him for the first deathblow. Lead him to the previous area so none of the other enemies interfere.
He's basically Juzou the Drunkard again. Dodge his slow leg stomp and overhead swipes, get out of the way of his perilous grabs, jump over his perilous sweeps, and deflect everything else. Deal the second deathblow and you'll receive the last Prayer Bead (40/40). Head back to the Sculptor's Idol and redeem four prayer beads for the Final Prayer Necklace and a trophy will unlock:
There is not much left to do in this playthrough. You still need to kill two Shinchimen Warriors, kill an optional boss in the Ashina Outskirts, kill Owl in Hirata Estate, and then kill the final boss.
You definitely want Phoenix's Lilac Umbrella, a prosthetic tool upgrade, for the Shichimen Warriors as it can block all of their projectiles.
Travel to the Poison Pool in Ashina Depths and head to the cave where you fought the Guardian Ape for the second time and you'll see a ghastly purple enemy in the area.
This is a Shichimen Warrior (VIDEO), an apparition-type enemy that will only take normal damage when you use a Divine Confetti. Use one, then charge in and attack him several times, deflecting his melee attacks as needed. If you get deflected, stop attacking as he will disappear and reappear somewhere else nearby. Look around for him to reappear, then close the gap but be ready to use the Lilac Umbrella to block his ranged blast (note that you can keep held to move around under the umbrella).
If your Terror meter starts to build up, use a Pacifying Agent.
After dealing the first deathblow, he will teleport away and repeat his pattern. Divine Confetti will likely wear off before you can defeat him so I use another one here. Continue chasing him down, blocking his ranged attacks with the lilac Umbrella, and attacking/deflecting until you can deal the second deathblow. Killing him earns you Malcontent's Ring, which is required for a prosthetic tool upgrade.
Travel to the Palace Grounds idol in Fountainhead Palace to kill a second Shichimen Warrior. Enter the building, then exit left. If you look down from the left ledge, you can see him in front of a waterfall far below. Drop down to the lowest ledge and prepare to engage him by using a Divine Confetti. Have the Lilac Umbrella ready to block his projectiles and kill him like you did the other to receive a Lapis Lazuli.
Travel back to the Outskirts Wall - Stairway idol, head deeper into the Outskirts, and you'll see Anayama and Kotaro beyond the next big building. Talk to Anayama and he will offer to sell you the Promissory Note for 1 sen, which reduces vendor prices by 10%. If you look ahead you'll see a path that leads further into the Outskirts.
Head that way and be prepared to deal with (or run past) a slew of enemies. From the top of a tower in the next area you can see a burning structure in the distance with the glowing blue light of a Sculptor's Idol below. The Ogre patrolling below can be killed with a single deathblow. Head to the idol and commune to be transported to the large area where you fought Gyoubu Oniwa on his horse early on. Commune/rest at the nearby idol before doing anything else. You'll see a giant thrashing enemy in the distance- this is the Demon of Hatred (VIDEO), one of the toughest bosses in the game.
He has three phases, each of which must be defeated by chipping away at his health until it is depleted, allowing for a deathblow. The Malcontent prosthetic tool upgrade can be used three times against him to stun him for an extended period of time and is best used during his third phase, so try to get it before this battle. If you want to beat him legit, you need to learn his attacks and understand how to safely and efficiently counterattack.
The key to this battle is patience. Do not overcommit- attack only as much as you are sure will allow you time to react to anything the demon will counterattack with.
From the start, rush up to him and attack four or five times, then be ready to react. These are his main attacks during this phase:
1) Slow single leg stomp: deflect, then attack ONCE.
2) Faster two leg stomp: deflect both, then counterattack two or three times.
3) Huge jump (camera shifts) to fiery slam: run away immediately, then grapple to him and attack a few times.
4) Right to left sword slash, left to right slash, foot stomp, sword slash: dodge the first two slashes (you need to find the timing to dodge these), deflect the stomp, then run at him towards his left side to avoid the final slash and attack a few times.
5) Slightly slower right to left sword slash, then overhead slash: dodge the first slash, then run at him and attack a few times.
6) Head slam, then possibly two followup head slams (with odd timing): deflect the first, wait to see if more are coming and if so, deflect. Counterattack a few times when it's safe.
7) Left-hand smack: this comes quickly. Deflect it, then quickly run at him with a slight left angle to avoid the follow-up attack and get a few attacks in.
8) Perilous charge: jump to the left to avoid his outstretched hand, then run towards him but try to keep about 50 feet of distance as he will follow up with a lob of fireballs that you want to run back/left to avoid. Try to maintain enough distance to bait a giant double slash- right to left, then left to right- followed up with a slow overhead slam. If he does this, try to run towards him left of center to avoid the second slash, then keep running towards him with a slight left angle to avoid the overhead slam. He recovers slowly so you can get four or five attacks in if you're close enough in time. He may only do the overhead slam, so be prepared to dodge left if necessary as you close the gap. If you're too close after the lob of fireballs he may repeat this attack. He may also do the overhead slam by itself so run towards him with a left angle, dodging if needed, then get to him and attack a few times.
9) Shower of several tracking fireballs: run and circle left, trying to angle it so you are circling inward slightly (not too much or you'll get hit) to close the gap. Do not stop moving or you will get hit, making it hard to avoid the follow-up fireballs. When he stops, run to him to get a few attacks in.
If he leaps away, react as if he had done the perilous charge by creating adequate distance in preparation of his giant double slash.
When his health gets to about 2/3 and then 1/3 he will stagger briefly, allowing you to get in five or six attacks.
After you deal the first deathblow the second phase will begin. He will start with an area of effect explosion, so stand back, then charge in after it goes off and attack a few times.
The key difference in this phase is that after he creates distance, he will almost always go into sort of a yoga pose, followed up with a slam on the ground that sends a wave of flame at you. Run to either side (I usually go left), jump to avoid the flames (you need to find the right timing), then grapple to him and attack a few times. The rest of his attacks are pretty much the same.
After you deal the second deathblow, run away. Far away. He may chase you to get to the center of the area where he will first do a series of perilous sweeps, then create a ring of fire. I get far away from him to end up outside this fire ring. He will then charge at you and do a lunging attack which is best avoided by keeping an adequate distance. Run in and attack a few times, then continue as you had with previous phases. Be careful with perilous charges as he usually follows up with a second that you must also jump over to avoid. The main difference in this phase is that he may do the perilous sweeps and create a ring of fire again.
Malcontent can stun him for a long time if you use it with good timing. This will allow you to get 10 to 12 attacks in and can be done three times, so definitely save it for phase three. After you deal the third deathblow you will get the prompt to deal the Shinobi Execution, killing the Demon once and for all. A trophy will then unlock:
You'll also receive Memory: Hatred Demon and the last two Lapis Lazuli. Head to the Sculptor's Idol and enhance attack power with Memory: Hatred Demon to permanently increase your attack power (from 11 to 12).
Note that there is a cheese to beat this boss in about a minute (VIDEO), but defeating him properly is so much more rewarding.
Next, travel to the Hirata Audience Chamber idol in Hirata Estate and prepare to battle Owl (Father) (VIDEO), the most difficult boss yet.
Owl's attacks are relentless and brutal. Like with the previous battle with him, prepare for a long affair where you chip away at his health over time. You must understand how to react to all of his attacks as one single mistake can result in being pummeled and killed.
He has two phases which are similar but the second adds some new attacks.
Like with many other battles, focus on attacking him until getting deflected, then reacting. Here are the attacks he will use during this phase:
1) Two shuriken toss followed up by a forward flip sword slash: guard/deflect the shuriken, then dodge forward just to the right of him to avoid his slash and follow up with a whirlwind slash to hit him twice.
2) Charging perilous sweep: jump back and left and you should land near him, allowing you to get a few attacks in. He often follows this up with a slow overhead slash- attack him a few times, then dodge to his right to avoid the slash. If you dodge too quickly he will instead do a horizontal slash that will hit you.
3) Kick to backflip away: he doesn't usually follow this with anything immediately, so just be prepared for whatever he does next.
4) Multi swipe combo: deflect these, then counterattack. He sometimes follows with the charging perilous sweep.
5) Firecracker throw to perilous thrust: can be hard to see because of smoke from the firecrackers, but Mikiri Counter the thrust.
6) Slash/shoulder charge combo: this comes fast and is very dangerous. Deflect the slash/charge/slash and immediately dodge (or run) forward and to his right to avoid the firecrackers and the final slash, then counterattack.
After you wear him down and deal the first deathblow, phase 2 will begin. He has a few new tricks during this phase. You will notice a blue owl flying around now and he will sometimes disappear, then reappear from the owl and pounce. When you see him disappear, run away from the owl until he reappears, trying to maintain distance so his attack doesn't hit you.
For his other new attack, the owl will land on his outstretched hand and turn red, after which he will hurl a wave of fire at you that you need to run and jump to either side to avoid. He will follow this up with a perilous thrust that can be Mikiri Countered, but I usually just ran far away to avoid it entirely.
He will now throw shuriken when he does the kick to backflip, so deflect those to avoid taking damage. Other than that, this phase is the same as the first so carefully wear him down until you can deal the second deathblow, after which you can perform the Shinobi Execution.
Upon defeating him, a trophy will unlock:
You will also receive Memory: Foster Father and the Aromatic Branch, which is the item needed to reach the Purification Ending. Commune with the Sculptor's Idol and enhance attack power with Memory: Foster Father to permanently increase your attack power (from 12 to 13). All that remains is the final boss who can be accessed via the secret passage in the Ashina Reservoir. Travel to that idol, then go down the steps and run out onto the branch on the left. Grapple across to the left, then run out onto another branch and jump across to the platform ahead (grabbing the ledge if necessary). Drop to a ledge along the wall, then grapple straight across (under the bridge).
Make your way down to the platform with the Sculptor's Idol to commune and rest, then open the door next to it with the Secret Passage Key. This may look familiar as it is the place you met Kuro in the beginning of the game. Run through the tunnel and into the open field to trigger a cutscene, after which the final battle will begin (VIDEO).
This battle consists of four phases- the first is against Genichiro (similar to the battle against him in Ashina Castle), then three more are against Isshin Ashina. This is definitely the most difficult battle in the game and will require practice, patience, and persistence to succeed.
For the Genichiro phase, run right at him and he will wind up with a devastating slash that you can avoid by getting behind him. He sometimes follows this up with a second such slash that you can avoid by dodging through it at the right time. Your main strategy here should be to attack until you get deflected (usually twice), then be ready to react (usually deflect) and repeat. If he simply counters with a single sword slash, deflect and counterattack. If he does a perilous sweep, jump over it and counterattack. If he does a perilous thrust, Mikiri Counter it. If he jumps straight up, you can either deflect his downward slash and possibly Mikiri Counter a followup perilous thrust OR simply dodge his downward thrust and counterattack. He will occasionally try to jump to the side to shoot his bow but if you're following the attack/deflect pattern, you should hit him mid-jump. He will sometimes wind up for a long sword flurry combo so either try to deflect it all or, better yet, deflect the first few attacks and then back away until it's over. This part of the battle is by far the easiest and shouldn't present any challenge at all.
After Genichiro is defeated, a cutscene will occur and the battle with Isshin Ashina will begin.
You must perform three deathblows on Isshin and each of his three phases are more difficult than the previous one. For his first phase he has several attacks with just a sword:
He does different one, two, and three-swipe attacks after deflecting that you want to deflect, then counterattack. You will need to figure out which pattern he is doing so you know how many attacks to deflect before counterattacking yourself.
He has two attacks that start by putting his hand on his sheathed sword. As soon as you see this happening, guard. The first comes quickly and is followed up with a perilous sweep- guard the first attack, then jump over the sweep and counterattack until you get deflected (GIF). The second has a much longer buildup and is a fast double swipe with long range that you want to dodge through as soon as you see the flash of light by his hand indicating that it's starting, then punish him until you get deflected (GIF).
He may kick you away and if he does, be prepared to Mikiri Counter the perilous thrust (GIF).
He may do an overhead slash that hesitates briefly- dodge to the side, then dodge the follow up slash and counterattack (GIF).
He may also do a charged attack that releases a burst of energy straight ahead, but be careful as there is another pulse around him a second or so later (GIF).
He has a charging attack that usually happens when you create some distance. Healing is tough because he is so relentless so you either need to take a chance and hope he doesn't smash you while you're healing or run far away to heal, likely allowing his posture bar to deplete.
For his second phase, he will stomp the ground and pull out a spear. He now also has a gun(!) that he will fire at you seemingly out of nowhere. His spear affords him a much greater range and his attack combos will be different than in the previous phase. Don't attack more than twice (or just once to be safe) even if your attacks aren't deflected as he will almost always counterattack after your second attack. Watch for him to jump backwards and slash with the spear, which can be a deceiving motion. He will occasionally do a long combo with several spear slashes ending in a perilous thrust that you want to Mikiri Counter (GIF). He also may shoot you, then do a perilous attack (sweep or thrust), so respond accordingly.
He has a very dangerous charged attack that hits in a huge arc around him. You can either try to time a dodge and avoid it (very difficult to do successfully), quickly run out of range, or hit him with a firecracker to interrupt him.
His third phase is similar except he now will add a perilous lightning attack. When he does this, be prepared to jump and get hit by it, then press 
to do a lightning counter before landing (GIF). He has new different charged attack that shoots out two consecutive bursts of energy straight towards you- dodge to the side to avoid them (GIF). He also has some different combo attacks that you'll have to work out deflect timing with. He is frantic and relentless in this phase.
Again, being able to recognize what he is doing quickly and then reacting properly is the key to defeating him. Each time you take damage, ask yourself what you should have done differently and try to react that way the next time.
Once you deal the third deathblow, you must perform the Shinobi Execution, after which you'll have control and Isshin will be kneeling on the ground. Go behind him to perform a final deathblow, after which a trophy will unlock:
You will also receive Memory: Saint Isshin and the Dragon Flash skill.
If you want to get multiple ending trophies from this playthrough, quit the game and make a backup of your save file. Then reload your game and you will still be in the flower field after having defeated Isshin. Interact with the Divine Heir and you will have three choices; each leads to a different ending.
After making your choice, the ending cinematic will play out, then the credits will roll. Once the trophy unlocks, quit the game, copy your save file back over, and reload your game to choose a different ending. After getting the third ending trophy, skip the credits and you'll be given the choice to start the next playthrough. Choose no and you'll regain control at the Dilapidated Temple. Commune with the idol and enhance attack power with Memory: Saint Isshin to permanently increase your attack power (from 13 to 14).
Unless you have anything specific you want to take care of before moving on, choose to start playthrough 2 from the idol.
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