The goal of PVE are:

  1. Levelling up your agent to get gold, better stats, unlock more features.
  2. Levelling up your Heroes to unlock skills, get better PVP bonuses, make PVP/E easier.
  3. Obtaining better gear for both PVP and PVE
  4. Obtaining CPs to get more heroes

While the goals above are not mutually exclusive, your strategy should vary depending on where your priorities are. As I have purchased every purchasable hero, obtaining CPs is no longer a priority and hence I no longer play 4.4, which is probably the best CP farm to date.

With my agent at level 237, it is relatively pointless to worry about levelling my agent, although the additional gold and the free energy refill is always nice. But as goal #1 is very closely tied to goal #2, and since I still have quite a few heroes at level 11 or below, this is important.

But not as important as #3, especially with the latest patch emphasizing your hero armory. The best things to slot are the silver weapons given in deploys, such as the P.E.W. Dingo(1175/893), Dragon(1332/771), etc. Generally, as a non-cash spender, anything better than the Spec Op stuff they sell is something that should be considered for slotting (in Spec Op 6, it's the Pyramidion, 637/637).

Thus it is important to farm the latest mission as they give the most xp and best equipment, in this case 10.6 or 9.6, and have all the heroes for deployment. For 10.6 the requisite heroes are Daredevil, Ironfist and Luke Cage; for 9.6 it's Ms. Marvel and Dr. Strange. Again, if you are still short on CPs and not have these pre-requisite heroes, you should farm 4.4 (Storm/Invisible Woman) until you have them.

It is just my personal preference to five-star all missions before farming. The gold weapons are generally useless, but the free gold at four stars is really worth it, as are the guaranteed CPs at 5 star mastery. Also, most missions have mission-specific equipment that can only be gotten at the particular level, and having that choice is always helpful.

Once that is done, you now can farm. 4.4 if you're still very short on heroes, 9.6 or 10.6 if you have the pre-requisite heroes to take advantage of all deploys.

10.6 is, in my opinion, much more difficult than 9.6, especially when 3 birding Elektra with all the mini-bosses. Luke, a scrapper, will have a hard time defeating Elektra who is flanked by two Bruisers which really limits the heroes you can bring into combat. But before we discuss 10.6, I'd like to discuss 9.6 since it is very uniquely suited for levelling a bunch of heroes without worrying about their classes and counter classes.

The mindless ones in 9.6 have three very annoying properties. One is that they take on the class of the first hero/agent that attacks them (if they're not a generalist), two is that they are mindless, and three is that they use the Abyssal stare which can get seriously harm you. The second one makes it difficult to use Emma or other psychic dependant heroes on them but generally harmless. The first one is very exploitable as you can force the mindless ones into a class that you wish. As for the Stare, there are many ways to prevent this, most notably by equipping your hero with items that makes him immune to bleeding/poison(i.e., techno-organic endoskeleton). If you add a Hoarfrost Mace that makes the agent protect, you will never have to worry about the stare again. Otherwise, just use up all the items that you have piled up that deals with poison/bleeding and you'll be fine except for very extreme circumstances.

You want two things:

  1. A hero with an area attack that will turn every mindless one into the hero's class
  2. Another hero who can take advantage of the class change above.

The trick is to make Hero 1 go before Hero 2, and this can be accomplished in the following ways:

  1. Recharging, using an item, or using a buff skill that does not affect the mindless ones if Hero 2 goes first
  2. If your agent goes before your heroes, and Hero 2 is set to go before Hero 1, use the Quantum Jumper.

The easiest way to accomplish this is pairing Scrapper Quicksilver with a bruiser. Quicksilver will always go first, so the bruiser can have his/her way without worrying about going first. Captain America used to be able to do this as well, but he was nerfed :(

For the fight with Dormmammu, there are a few approaches you can take:

  1. Using the Torch - he is immune to the Flame of Faultine and Armageddon's burning, making it easy to combat Dormammu.
  2. Using the same approach as dealing with mobs, making Strange either Hero 1 or Hero 2.
  3. Just plowing through.

If your agent is well equipped, you should be fine with strategy 3; if you are having a lot of trouble, I would suggest using Torch.

Remember to do all the deploys and look for red fights (more xp for energy spent), and within red fights, those with 3 mindless ones instead of two groups of two.

10.6 is a bit trickier as you'll face a variety of classes. You still want to look for the 3 hands in one wave, but if they're not available, two waves are good enough. Stay out of three waves if you can, because it just takes that much longer. Also, unless you have a bunch of heroes, you'll find yourself short on scrappers as the mission just requires scrappers for the deploys. 

The truly tricky part is the face-off with Elektra with all the mini bosses, as you'll be facing a wave of three hands, two scrapper/tactician mini-bosses, then Elektra with two Bruiser mini-bosses. You are inherently handicapped with Luke being a scrapper and Elektra making everyone bleed (and cannot be removed with normal items that stop bleeding).

While any class and any hero will eventually work (good luck with three scrappers though), I had the most success with the following:

  1. Bruiser - try to carry over bruiser bonuses from the previous rounds as the first and second waves both feature one scrapper.
  2. Protecting non-scrapper - Captain America, Bruiser Collossus, Hercules, Bruiser Thing, and Phoenix can all keep the two bruisers away from Luke and prevent them from getting bruiser bonuses, except for an occasional overhead smash.
  3. Beast/Valkyrie/Cable - generalizing bruisers and/or removing counter attack from Elektra is good.
  4. Blaster - just plow through bruiser defense bonus. Not as efficient as the first two, but still much easier than employing a Scrapper/Tactician (Elektra counter attacking everyone is not fun). 
  5. Infiltrator/Generalist - try to carry over the counter attack from the previous round. If not, still better than bringing a scrapper or a tactician into battle. 
  6. Use of items - you'll have tons of silly stuff you'll never use; use them during Luke's turn as he's just bound to hurt himself attacking. Kunai Barrage, even at the lowest level, applies bleeding to all three of them. Anything that debuffs the entire opponent is worth hurling. 

The Ring, Sigil and the Sai are all better than the Mead/Pyramidion, so the final roulette also gives you a chance to upgrade your armory, making it more attractive than 4.4 which doesn't give you anything slottable other than the very rare Damage Amplifier and Combat Acceleration Program.

Lastly, be prepared to cycle through 4.4, 9.6 and 10.6 as you level up heroes that are required for the respective missions. Try not to waste precious energy and xp by employing Invisible Woman in 9.6 or 10.6, for example, as she is required for 4.4 boss fight and will be forced to gain xp. Same goes for Luke and Strange; leave their levelling to their respective missions for maximum efficiency. 

Even then, though, you will find that they'll be plowing through the missions long after they reach level 12.

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