Even though there is no single best way to obtain Mother Boxes, there are more than a few ways a player can earn them. If a player enacts on not only taking advantage of one of two of these methods but all five of which, then they will get the most number of Mothers Boxes as they possible can get. The more Mother Boxes they receive, the more chances they can get at earning even more Gear.
The 5 Ways of Farming Mother Boxes Include:
1) Story Mode. You will earn a Mother Box after defeating each and every chapter in Story Mode, with better Mother Boxes coming as you progress further. In total, more than 25 Mother Boxes can be earned here.
2) Joining A Guild. Sure, you can create your very own Guild where others can participate in, but by joining a crowded one that's already active will yield massive amounts of Mother Boxes. It's even easier than you think, as you will join a gang of other players working together to earn the same reward.
3) Multiverse Mode. By earning enough points in each series of fights on different Earth's, you will receive Bronze, Silver or Gold Mother Boxes. You can even earn all three from one series of fights if you score high enough.
4) AI Battle Simulator. This is one of the more easier ways of obtaining Mother Boxes, and there are two ways to obtain by doing so. The first is to create a team of defenders and wait for someone else to challenge that certain set of characters. If you're team of defenders lose, you will receive a Bronze Mother Box; if they win, you will earn a Gold Mother Box. The second way is to fight defenders that other people have made with you're team. Again, whether your team wins or loses, you can earn up to 5 Mother Boxes a day with this.
5) Daily Challenges. Each and every day, you will be given a set list of challenges you can personally complete (top right of the menu screen). These little challenges will net you a couple of additional Mother Boxes while playing, so remember to keep these tasking while you do.