Infiltrate the flying base is the first mission in Going Commando. After recruited as a Megacorp commando by Abercrombie Fizzwidget, Ratchet was sent to the flying lab in sector seven on planet Aranos, to retrieve the experiment from the Unknown Thief. Along the way, Ratchet had to fight the Thief's Megacorp security forces.
This and the following missions are the only missions in which the player can explore this path in the flying lab, as the later revisit to Aranos involves an entirely different path.
The starting area before taking the elevator upwards provides a good opportunity to become familiar with the controls. Ratchet is equipped with the OmniWrench 8000, the Lancer, and the Gravity Bomb. The OmniWrench is a melee weapon automatically tied to , which leads to a single swing of the wrench. Hitting it three times leads to the multi-strike, which can be aimed if the is used. By crouching with and hitting , Ratchet throws the wrench forward in a comet-strike, and it automatically returns to him, regardless if Ratchet has moved since throwing. Finally, the hyper-strike is activated by jumping with and hitting . Using the OmniWrench is completely free, and will cost no bolts since it is just a melee weapon. However, keep in mind that the OmniWrench does not upgrade with use.
The Lancer and the Gravity Bomb are both ranged weapons with limited ammo. Equip either using the quick select (hold and select with the ), or through the start menu. As a rule of thumb, you want to use your weapons in almost all situations over the OmniWrench, as weapons will gain experience as you defeat enemies with them, and will eventually upgrade. The Lancer is a rapid fire, mid-to-long ranged weapon, which is versatile and capable of handling most of the enemies in this mission and the next few. It upgrades to the Heavy Lancer, with much more ammo and an improved rate of fire. The Gravity Bomb, on the other hand, is very powerful and will easily kill any normal enemy hit by the blast in the first few levels, but has very limited ammunition than the Lancer, meaning it should only be used in tight spots or against clusters of enemies. It upgrades to the Mini-Nuke, a powerful weapon with a wider blast radius.
You begin the mission by taking the elevator upwards to the next room. First, smash the crates that are stashed near the entrance, as they contain bolts. Next, equip the Lancer and fire at the Megacorp Security Robot I - Chainsaw Models, ensuring you hold down or while doing so, as this allows you to strafe and aim more easily. These enemies can only attack in close range with their chainsaw, but are very weak and will be killed by a few Lancer bullets. Climb the ladder and break both the crates and the ammo crate (which will restore the ammo on any random weapon that is not yet full) and head left through the next corridor, killing the MSRs. At the end of the corridor, you will find a Megacorp Security Robot II - Flamethrower Model, which is very similar to the MSRs, with the exception of its choice of weapon; avoid getting too close and fire a few Lancer bullets at it. Break the glass nanotech crate, if need be, to replenish any health you have lost.
In the outside area, you will find MSRs and also new PX6 BladeBall enemies. These are small enemies that will rush in, land nearby, and then attack with blades by moving in your general direction. Though they can easily be dispatched with the OmniWrench, simply use the Lancer instead in order to upgrade it faster. Also, you can break the small, blue lights surrounding this bridge with the wrench, as they will also provide bolts. Head through to the next room and use the elevator upwards to find a cluster of MSRs. Equip the Gravity Bomb, and try to use it against all four MSRs at once (if you miss one or two, finish them off with the Lancer). Enter the door to the experiment room. Approach it and watch the cutscene to finish the mission. This will continue in "Escape the thief's security robots".