You must be cautious at all times. Go through the base a little bit and run back at the entrance. The aliens will come in 1, 2 or 3 at a time, kill them until no more will come. Then find a staircase and on the upper level, follow the path to get closer to the commander by following the commander symbol (which looks like an alien with a red nose), killing aliens along the way. Locate the room with another staircase leading upwards. Depending on the difficulty, there will be a couple of aliens (on hard mode, there are 3, including the commander). Kill them all, walk over the commander's corpse to grab the data.