I don't really agree on doing the second last battle (or the last battle) to be the quickest way to earn core energy.
Sure, doing the last battle story wise, will give you 35000 core energy (+ additional depending on final score bonuses such health, combo hits and buildings destroyed) but only the first time you beat the final boss.
Doing this a 2nd time, will net you only 10000 core energy instead of 35000.
Doing the boss battles over and over again, takes a good amount of time as well.
Even with a fully upgraded Maxus Dragonoid it takes a couple of minutes to defeat the boss for "only" 10-12k core energy.
In my opinion, the fastest and easiest (but also most boring) way to farm core energy, is this :
- When you enter the Vexos Base for the first time, you'll see a long hallway with a robot on the right side and a bit further on the left side.
- All you have to do is this: just walk straigth ahead picking up the blue and yellow core energy (go stealth by pressing

when you enter the danger zone)
- Once you get to the two barrels on both sides of the hallway, aim and throw at it. In each barrel you'll have 3 red core energy.
-
DO NOT PROCEED TO THE FLAG!- Once you've picked them all up, return to marucho's plane (press

button, then select it from the menu) and repeat the whole process.
Doing it this way, I was able to net 8200 core energy in less than 1 minute.
Any suggestions to improve this guide are welcome!
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Good luck!