Yo! It's been a long time in the making, but I finally posted the first draft of the storyline on the Commando website. It's a bit rough on the edges, but it will serve as a building block for things to come. Being an overview of the story, some spoilers are to be expected.
Here is a preview:
OPERATION: RAINFALL
April 12, 1996
Location: Arumäe, Estonia, 0300 hours
It’s the deep in the night and it’s pitch black. The objective is to get in the Nod base without too much noise and download the data from the Nod Comm Centers’s main console and then sabotage the main console, rendering it inoperative. Once Jack has done that, he must escape the base and evac via GDI Chinook helicopter.
This is based on a Renegade mission that was removed from the game before release. The only remains of that was a cutscene of a version of the game that was sent for press reviews. Here's a video of the removed cutscene in action. Also, the very first E3 Expo preview trailer of the game featured a similar setting.