Thought I may add my knowledge of NG2's mission mode to this as well. This is my first guide so bear with me. I'm also assuming you have a good knowledge of the game and its combos, as there is no point attempting this unless you've beaten Master Ninja story at least. MN campaign is a pushover compared to this.
There are 3 missions that I would consider the hardest: 8, 12 and 14. If you can do these 3, you can get the 1250. In fact, if you can beat 14 you can get the 1250. I'll only be covering these 3 missions, as covering all 16 in depth would take a large amount of text. Many enemies in these 3 missions will reappear in others anyway.
3rd worst: Mission 8.
Mission 8 pits you up against Fiend Genshin and rocket launcher minions. What's so hard about this compared to 4-7 you ask? For some reason, Team Ninja took away all healing items (you would normally get 1 Grain, 3 Herbs in other boss missions), and made it so you can't use Incendiary Shuriken. Add to this that you're in a small, cramped arena with a bad camera and the problem increases tenfold. You need to play defensive against Genshin, but the arena simply doesn't allow for it. The rocket guys spawn in on 100% health of Genshin, then 75, 50 and so on. If you "skip" the 100% guys and kill the 75 guys, the 100% minions will still spawn in.
I used the Kusari-gama jump YXY for this fight. Jump YXX also does the same thing IIRC, but I prefer Jump YXY as it's the same input as the claws FS > ID, so it's easier to remember. Genshin's AI will not attack you until you land on the ground after the final hit of the combo for some reason. All I can say is exploit it. Dodge Genshin's attack, and respond with an AYXY whenever it feels safe. If you're in a tight spot, you can also use the KG's Counters on Genshin. They don't do much damage, but they stun him. Think of it as an improvisation move. You could also use the Lunar for this fight, with its Counter Y attack. It's pretty easy to counter him once you've got it down, and it does a bit more damage than the KG's counters. Don't spam Y after the counter, otherwise you'll go into an aerial attack that will miss Genshin 99% of the time and you'll get punished for it. Just hit Y a couple of times after the counter and you'll get a few hits in but stop before the aerial hit. You can also use the infamous XXY on him if you want. I prefer the KG however, as Genshin cannot handle the AYXY for whatever reason.
As for the rocket guys, you are given 1 ninpo at the start of the mission. I use it as Inferno on the rocket guys as soon as the mission starts. This way, you get a free 25% of his health with no rockets pelting you 24/7. To have a hope of winning, you should generally be taking very little damage, if any, until the rockets spawn in at 75%.
Also of note is the boat. It's located at the back of the arena, and provides a height difference. Genshin really wasn't designed to handle the boat, thus you can semi-cheese him with the height difference. Some of his attacks won't be able to hit you if you're on the boat. It's more RNG based than anything however, and good skills with the KG AYXY will generally outperform the boat cheese. I used the boat cheese to beat it on Mentor, but for my MN run I took the straight up KG approach. This mission isn't so hard as it is frustrating. The camera will annoy you to hell.
2nd worst: Mission 12
Mission 12 puts you against the Four Greater Fiends and Fiend Genshin one after the other, while receiving an item in between each fight. The order is Alexei, Volf, Zedonius, Elizebet, Genshin. You are given 3 ninpo, 1 grain, 3 herbs when you start, and more items are handed out along the way.
Boss 1: Alexei
Alexei is where 75% of my deaths came from. Not because he's challenging, just because I wanted to conserve my items right at the beginning. I was using no items during this fight on my attempts. The best combo I found was XY OL 360Y with the Blade of the Archfiend. This isn't a combo listed ingame, it's a freeform combo. The XY does good damage, and the Y launches you into the air. The on landing 360Y hits like a truck and has RIDICULOUS i-frames in it. The general strategy is to dodge his combo and respond with an XY OL 360Y. It's almost impossible to explain how/when to dodge in words, the only solution lies in you actually playing for yourself and gaining experience of his patterns. For his tornado attack, you can time your 360Y as he's charging and you will take 0 damage. Don't do the XY first, just jump. The i-frames are just that good. When he gets to berserk mode (triggered by roughly 25% hp left), he has 100% i frames while "powering up". His combos will be a lot longer and could possibly 1 shot you. He'll tornado at you up to 3-4 times in a row and absolutely destroy you. You seriously need to put Alexei down fast when he goes berserk, or you'll be seeing the Game Over screen. I just timed the XY 360Y so when he finishes charging, the Y and 360Y will connect with him. You can also use the Tonfa 360Y just for catching him as his i-frames end, it does crazy damage if it all connects, and it has even crazier i-frames than the BotA 360Y. It's a risky strategy though. Of honourable mention, the KG AYXY can also work for the entirety of this fight. Alexei can handle it way better than Genshin though, be warned.
Recommended item usage: Nothing. Use a herb to restore the red health after the fight if you need it. If you're just getting used to Alexei's (infuriatingly grab-happy) AI, then use a Grain or whatever you feel like to pass. No point restricting item usage if you only just started attempting the mission and have no hope of completing it yet. I started restricting my item usage on Alexei when I could reach Elizebet occasionally.
Chest Reward: 1 Grain
Boss 2: Volf
Volf is probably the easiest out of the 5. He'll still gladly take off 90% of your health in one shot if you give him the chance though. Best combo for him is probably YYYY with the BotA.
If you go to the opposite side of the arena, he's almost guaranteed to do his running charge at you. All you have to do is dash to the side at the right time, land a YYYY on him, run away, repeat. The timing on the dash is the single hardest thing about this strategy. It's a very weird timing that will probably take hours to reliably get down. If the first couple of Y's don't appear to be stunning him, just run to the other side of the arena and repeat. If the Y's aren't stunning then you were probably too slow to attack him and he's starting up a combo that has hyper armour. (Hyper armour is the ability to not be stunned).
On occasion, Volf will do a different move when you're on the opposite side of the arena to him....
If he does the Scythe UT, just dodge it. Nothing you can do. Get to the other side of the arena and try again.
If he does his 2-handed charge at you, you might be in for some trouble. The timing to dodge it and respond with YYYY is even stranger, as he moves slower in this attack. You could try dodging and attacking if you're lucky/stupid, but I would just get the hell out of there and try again.
If he does the jump attack, you can dodge it similarly to the regular running charge and respond with YYYY. I never had a problem doing this and he very rarely hit me.
Recommended item usage: nothing. If you do get hit with a running charge and somehow survive, just heal up the red with whatever items you need to after the fight. There's no point healing mid fight unless you're just getting used to Volf. Basically, don't heal mid-fight on a serious attempt to beat all 5, if that makes any sense.
Chest Reward: Lives of the Thousand Gods (LotTG)
Boss 3: Zedonius
Ah, Zedonius. Here's where it starts to get interesting. Zed will constantly spam fireballs and grab you, dealing ridiculous damage and may possibly even hand out 1 shots. Best move would be, surprise surprise, YYYY with BotA. You could use the Scythe YYYY, but i'll explain why I prefer the BotA later.
The biggest key to success when fighting Zed is to be able to dodge his "aerial slam" attack. I don't really have a better name for it, but I'm sure you know which one I mean. He comes out of the sky and lands by you, causing an AoE that will take around 80% of your lifebar off. If you jump at the right time, you'll dodge it and take no damage. Zed will also leave himself VERY open to a BotA YYYY or Scythe YYYY at this point.
Once you've hit him with the YYYY, he will usually walk around on the ground for a second. In an ideal world, he'll then try and grab you. This grab will probably deal another 80% of your life if it hits, but thankfully it can be easily dodged. He will again leave himself open for a YYYY if dodged. I've had a couple of times where he's got stuck in an AI loop and just tried to grab me every single time. This resulted in me killing him without taking any damage, just don't expect this to happen often. Dodging the aerial hit and his grab are the two main steps to beating him. If it goes differently, however, here's what I do...
If he does the sweeping laser attack, you can just 360Y right through it with the BotA. This is why i don't use the Scythe. You could also probably nail Zed with an XY 360Y if close enough. It's situational.
Same thing goes with the "earthquake" move. He will send out a fiery shockwave in one direction - towards you.
There isn't much else I can really say. If you're in trouble, you can also start using Ninpo here as a means of dodging his attacks and then landing a YYYY. I think Piercing Void does a bit more than Inferno, with him being the Ruler of Flame and all. As with all bosses, it's about knowing how the AI works. I can't offer much else other than telling you to practise.
Recommended item usage: As much as you need. Zed is where the run starts getting real, and even if you use everything you just might get super lucky on the next 2 bosses. Use whatever you need, including ninpo.
Chest Reward: LotTG (again)
Boss 4: Elizebet
Sadly, Liz is where my guide falls short. I'm really not good against her, but I might be able to tell you stuff you didn't know....
For a combo, I would use the Claws Flying Swallow. That is, A+X (press both at same time), then Y in midair. It does little damage, but it will stun her for a bit. You can stunlock her with this, as the stun is just long enough to chain flying swallows on her. The timing is very strict and I never managed to get it more than 5 times in a row. It's a good way of racking up damage. For the blood attack, if you flying swallow her, she will sometimes get knocked down to the floor. This is perfect, as there is a stunlock "glitch" that will keep her on the floor forever, unable to attack. As she's on the ground, swap to the Flails and keep pressing X every half a second. Not an XXXX combo, but wait just long enough so the hits aren't counted as a combo, just seperate hits. The timing isn't as strict as the FS stunlock I mentioned above. You can also Inferno her out of the blood attack, and I personally used all 3 of my ninpo here. Honourable mentions for combos include BotA 360Y (good for ocountering her melee with i-frames) and the Scythe XYY. Not the infamous jump XYY, but the ground one. Her AI can't handle it too well for some reason. Also KG AYXY.
Recommended item usage: Everything. If you've done Mission 8, Genshin should be second nature. Use as much as you need to see you through especially Ninpo. Ninpo sucks against Genshin.
Chest Reward: LotTG (yet again)
Boss 5: Fiend Genshin
If you've done Mission 8, this should be no problem. Use the same strategy as you did there. It's even easier because he has no minions with him. In fact, none of the bosses do on this mission. I can't give any more advice than what I wrote about mission 8.
Recommended item usage: EVERYTHING. There's no bonus for saving items. Use absolutely everything. I had 1 herb left over after beating Genshin because I got a good stunlock on Elizebet when I completed this mission.
Chest Reward: nothing. The mission ends after you kill Genshin.
Worst: Mission 14
Mission 14 is the harder of the two 100 fiend challenges. You are put up against 100 enemies that spawn in waves, with 3 herbs and 2 ninpo slots. The worst part is that 100% of damage is converted to red. On Master Ninja campaign and other MN missions, only 50% is converted to red. This is huge. Any damage you take will never be recovered unless you use a herb or get blue essence.
6 Black Spider Ninjas
6 Tac Ninjas
This is by far the easiest wave. They're just regular ninjas with no IS spam coming your way. Use whatever to take them out, I used Scythe UT's and AXXYYY if I had no essence to chain.
5 Black Spider Ninjas (with claws)
5 Purple Van Gelfs
This wave isn't too bad, and this is where we introduce the Tonfa. Tonfa UT's and ET's will absoutely destroy anything it touches. If it can be delimbed, the Tonfa will kill it.
Just charge up as wave 1 ends and spam Tonfa UT.
6 Rocket Ninjas
6 Silver Gajas
More Tonfa UT chaining here. The rocket guys can nail you out of your charging though, so don't just sit around charging. You need to chain to be successful.
3 Multi-Rocket Ninjas
3 Red Gajas
The multi rocket guys are really frustrating. Get to the opposite side of where the rocket ninja is and Tonfa ET each Gaja as it spawns. Watch out for rockets being fired at you across the map, but since you're so far away you'll easily have time to dodge. Once you've taken the Gajas out, dodge the rockets and stun the ninjas with regular shuriken. Never underestimate the regular shuriken, it can really stun them and stop them spamming rockets. Once up close, deal with them however you wish. I use a freeform variant of the Flower Garland Drop, which is YAXY. XAXY also works. Note that A isn't a jump, it's the Heavenly Justice move with the Tonfa. YAXY will almost certainly 1 hit kill them. I avoid using UT's and OT's because you might get some blue essence back if using regular attacks. XYXXXXY can also be used, this is an Izuna Drop.
6 Brown Werewolves
6 Red Gajas
More Tonfa UT spam here. After you kill one Werewolf, they'll start chucking body parts at you. Be careful.
4 Rocket Ninjas
4 Multi-rocket Ninjas
4 Humanoid Mechs
This is where it gets interesting. The multi rocket ninjas are a pain as always, and the Humanoid Mechs will destroy your lifebar in a hurry. This is where I bring out the Incendiary Shuriken. Tag 1 IS onto a multi rocket ninja, then OT him. You can use this essence to ET a mech. If all of the ET connects, you will take the Mech out instantly. You can repeat this process until they all die. If you don't have essence, you can dodge out of the way of the Mech's jump attack and you should have enough time to charge an ET without essence. Go nuts with your IS supply here, and be wary of the Mech's explosions after death.
4 Red Werewolves
4 Yellow Van Gelfs
4 Machine Gun Mechs
I HATE the Machine gun mechs. Try and get as far away as possible and Tonfa UT chain the Werewolves and Van Gelfs like before. Just note that the Red wolves have (slightly) better AI, and the Yellow Gelfs can really hurt if they pounce on you. Once you have just the mechs left, pull out the Scythe. A Scythe UT will outright kill a mech. If you have no essence, a few Scythe AXXYYY's will deal with them. Just remember to hit block after killing a mech, or you'll get caught in the explosion. There is absolutely no need for IS's after this wave, so use them all if you have some spare.
I used my first herb on this wave. Screw those Machine gun mechs.
12 Fiend Ninja Dogs
Anyone who's played MN campaign will know how infuriating dogs are to fight. As soon as you kill the last Mech of wave 7, charge up a Scythe UT. The plan is to UT chain the dogs with Scythe UT's and 360 UT's. When you inevitably run out of essence, use the trusty AXXYYY with the Scythe, and here's where I'd recommend you use Ninpo. I used 1 Inferno Ninpo here, as this will kill 3 dogs and allow you to build a Scythe UT chain back up. Other moves you could use are the Lunar 360 UT, and Dragon Sword 360 UT. If you have no essence and just do a 360Y, you can do 360Y XXX B and then go into another 360Y and repeat. The "B" input is with the regular shuriken. It's pretty hard to pull off, and I'd just recommend using the Scythe. I used my 2nd herb here, just as the next wave was spawning in. I also had 1 Ninpo slot left and 2/3rd's of my HP.
Wave 9 (final wave!)
4 Machine Gun Mechs
4 Red Dragons (encountered in Ch. 12 campaign and ToV9 MN, also ToV 6 MN?)
Try and get the Red Dragons away from the rest, as they tend to be very aggressive and almost as grab-happy as Alexei. If you did ToV9 on MN, you should have a good idea of how the Red Dragon's AI works. If not, you'll just have to learn. They have an annoyingly huge HP bar, and it takes a lot to stun them out of an attack. Use Scythe UT's (not 360), and AXXYYY.
AXXYYY is a very safe move, but doesn't take much off their enormous HP bar. YYYY will do more, but it's riskier.
You can wind path off their heads to stun them and get some free attacks in. Use everything you have here (although you probably won't have much) as this is the final wave. Aim your inferno at the Red Dragons if you have it. Be careful of jumping around the Marionettes. They have a ridiculous homing move that they can do from crazy distances that will strip off a majority of your HP bar. They'll only really do it when you jump. If you've done ToV4 on MN, you'll understand exactly what I'm talking about. If I didn't get hit with a stray Marionette homing attack on this wave, I probably wouldn't have needed to use my 3rd herb at all.
Once the Red Dragons are gone, you're pretty much done. Windmill Shuriken UT's will destroy the Marionettes, but this requires you to be fairly close. The safe strategy is to get to the opposite side of the arena and use Bow UT's. Focus on the mechs first, as the Marionettes are pretty docile if you're very far away from them and aren't jumping around.
I hope this guide for these 3 missions will help you, and make the exclusive 1250 NG2 club not so exclusive anymore. As you can see, typing out strategies for all 16 missions would take a stupidly long time. A majority of the enemies on these missions reappear in others, and frankly if you have the skill and intuition to do these, you should be able to use your own strategies or use other guides for the rest. Don't be fooled by the 5.5 TA ratio on this, it's way harder than MN campaign. Only the people who managed MN campaign will have purchased this DLC, and those people obviously have a very good shot of doing this.
Good luck! (You'll need it)