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There seem to be 2 different problems here, so just to be thorough here's what should happen when you are sent in to Mt. Gigas to complete some training (obvious spoilers follow).
1) Use your highest level IUF card on the training scanner. It should break.
2) Go to the back of the scanner, and touch each wire from left to right to reconnect them. Use your highest level IUF card on the scanner again, and it will instruct you to proceed to the Gunnery training.
3) Talk to Sgt. Rubble in the Gunnery section, he'll give you a rocket launcher and improve everybody's Modern Weapon skill to 10, and tell you to meet him in Covert Ops after taking some target practice. I've always gone down to the end of the gunnery range to explore the storage room down there, and when I return he's gone. I also take a couple potshots at the training dummies just for kicks.
4) Head to Covert Ops, and Rubble should be right inside the doorway. Do what he says, and go through the door on the right and follow the caves around in a loop, killing everything you see and collecting flags. After exploring everything exit through the door with the blue switch, which will take you right back to where you started. Rubble should be right where you left him, just inside the doorway to Covert Ops.
It's really that simple; I'm not sure what the original poster meant by asking where Rubble is after you complete the Covert Ops mission, because he should be right back where you left him. If he isn't, it sounds like a bug or something (maybe try reloading an old save game from before you entered the Upper Mt. Gigas map area).
Hope this helps...
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