About this Mother Base app:
According to my spreadsheet, up to mission 19 the enemy officer is a level 1 Commando, after that it goes through the MGS3 bosses in order, each with five missions, so in 20-24 you fight The Pain, 25-29 The Fear, 30-34 The End, 35-39 The Fury and 40-44 you fight Volgin. I haven't done mission 45 yet. I'm worried because I don't know which Metal Gear it will be, so far it has gone through the Peace Walker Metal Gears in order (except for Peace Walker) twice, the second time they've appeared as level 2, so it could be Pupa level 3, Pupa Custom (I guess), Peace Walker or something completely else.
The pattern dictates, though, that mission 45 will consist of The Boss (seems harsh as she's very good, but she is the next Snake Eater boss after Volgin), six level 5 commandoes, three level 5 MBT: Customs and a Metal Gear but I have no idea which one. I'm not too thrilled about my chances though as mission 44 was basically the same and I lost my officer, two level 5 heavy armour soldiers and a level 5 heavy custom tank... So I'll run it anyway and see what happens.
Ok, so I ran it. I lost The Boss, two level 5 heavy armour soldiers, a level 5 commando (I have no idea why he was there), a level 2 heavy armour soldier, two level 5 heavy custom tanks and one level 1 heavy custom tank. That was REX's fifth or sixth fight with a Metal Gear and it still hasn't levelled up. So, basically, it wiped out all my good stuff.
My prediction was right, The Boss was the enemy officer so she'll be the officer until mission 49 and the rest of their force was as I guessed, and the enemy Metal Gear was Peace Walker at level 2... Hilariously, one of my level 5 heavy custom tanks killed it in a single shot.
My Boss did 200 points less damage than the enemy Boss, so that's hardly fair. The way the combat works doesn't really make any sense anyway though since in one turn you damage them and they damage you back, regardless of whether or not they died. Most of my units died because the enemy had, like, 16 hit points left but they attacked me back and did 400 or more points of damage to me!