"How do you beat Aegis MKII?" is one of the most asked questions in Project Pokémon and on the wikia, second to only "Can you make more codes" or "What is the best team to beat E4 with"? The motive for beating the entity is very obvious, not only does he give 11k exp but he also gives over 200k Pokédollars on the first win and 17k after that (without booster). This is (in my opinion) the best strategy for beating Aegis MKII.
Perhaps the most key part of beating Aegis MKII is having a pokemon that can outspeed it. I recommend using Electrode, since he is easy to get and you don't have to teach Mewtwo or Deoxys Thunder Wave, saving you the purchase of a TM. Electrode will most likely already know Thunder Wave but you can you use the Move Relearner if not.
Electrode needs to be level 100, with a nature that boosts speed. He also needs to have max EV in Speed. You can do this by battling the robot in Saffron City; "iso_speed" 11 times. If you do this he should have a speed stat of 400-415. Make sure Electrode is in slot one when you battle him.
Use Thunder Wave on him first move. If you have done this correctly Aegis should have been paralyzed. Success. After this you can use Explosion to kill yourself if he didn't one shot.
Although she is optional it is highly recommended to use her, as she can allow you to 1 shot Aegis MKII, causing less chance for him to heal his paralysis with Repair. Jynx's job is to use the move Fake Tears (Teach with Move-Realearner if needed) on Aegis MKII. She will be able to attack first because of Aegis being paralyzed. "Fake Tears" lowers the entity's pokemon's Special Defense by 2 stats.
Jynx must be level 100 with Fake Tears. This is the only requirement because she is only using a status move on an already slow Pokémon. If he does not 1 shot her do not attempt to harm Aegis because this increases chance of him using Repair. Instead Fake Tears again until you have died. It is important not to switch out midway because he will attack first.
Chandelure/Volcarona/Victini/Mega Charizard/Strong Fire Type
The last step is to have a Pokémon with the move Overheat that can 1 shot Aegis MKII. Most strong fire types can do the job, I personally use Volcarona or Chandelure. Most people that are trying to beat him should already have a strong fire type anyways. They need to be able to 1 shot Aegis to eliminate chances of using Repair and curing paralysis. The only reason for his paralysis to wear off is if he is low and uses Repair, or if you are seriously slow, it can wear off naturally.
Level 100, best move to use is Overheat because it is an easy to teach TM and doesn't miss often. (In case it does bring in an extra pokemon that can 1 shot). They should be EV trained in Special Attack or they need to be seriously strong. You don't have to use a fire type but it is most effective against Aegis MKII. Simply, click Overheat and if it doesn't miss or if your Pokémon isn't too weak, Voila! you have beaten Aegis MKII. Collect your cash and you can use this same strategy again.
- Strong Fire Type With Overheat
This strategy is not time consuming and is very reliable because Thunder Wave and Fake Tears can't miss. Overheat can miss but you can clean it up nicely by bringing in your back up strong fire type to do the job instead, or you can try again and you'll have a 90% chance it will work this time. 90% Chance of Success with 3 Pokémon that arn't a major strain to catch.