Megaman Zero (Part 2.5)

After shutting down the disposal factory, a few new missions will open up to you, and you can do them in whatever order you prefer. As you complete missions, others will open up to you usually re-using the same area but with new enemies and a different boss. There are also two interlude missions that you will get after you have made a certain amount of progress.

You may want to consider leaving the "Retrieve Data" mission for near the end, because the spider nests in the underground lab are (unfortunately) one of the best ways to farm energy crystals. It's a long and tedious process, but so is every other method. The nests will not be available to you after completing the mission. Leaving it until near the end means you won't get the Triple Rod or Shield Boomerang until almost the end of the game, but I find you don't really need them anyway. Alternatively, you can gain a decent amount of energy crystals from the Hidden Base area after you clear it out.

Once you've completed all four desert missions and "Rescue Colbor" you can use the Trans Servers to alternate between the Desert, Subway, and Resistance Base for fairly quick access to 56 EC in each rotation. Also be sure to listen to Andrew's second story all the way through after your very first (chosen) mission and you will receive 500 EC. If you do a second mission before speaking to him you will never be able to do the event.

Mission Set 1

1A: Destroy Train (complete to get 1D)

1B: Find Shuttle (complete to get 1E and 2B)

1C: Retrieve Data (complete to get 2A)

1D: Occupy Factory (complete to get 2C)

1E: Find Hidden Base (complete to get 2D)

Interlude 1: Defend the Resistance Base

Mission Set 2

2A: Rescue Colbor
2B: Duel In the Desert 

2C: Protect Factory

2D: Stop The Hacking

Interlude 2: Defeat the Intruders