Break into Megacorp Headquarters is the penultimate mission in Going Commando, taking place in the Protopet Factory, Yeedil. Ratchet and Clank met up with Angela Cross again in her home on Grelbin, where she discovered that all Protopets were being produced as clones of the original Protopet in Megacorp's Protopet Factory and headquarters on Yeedil, and that by defeating the original, they could shut down Protopet production. As she had her old Megacorp ID badge, the three would be able to infiltrate the facility, though they agreed to go separately to sneak past Megacorp's orbital defenses.
Two platinum bolts can be obtained during this mission, one at the very start, and one at the very end.
This is a lengthy mission filled with combat, so ensure that you are prepared. All weapons should have been purchased by now, if not upgraded. The Shield Charger should be turned on at all times for the extra defense, and if needed the Kilonoids and Megaturret Glove can provide useful support. Though the Electrosteel armor is not an absolute requirement, it should bought if you are struggling. Another option is to obtain platinum bolts and use them to purchase weapon mods for all your weapons. The Plasma Coil will be useful for when you run into multiple enemies, whereas the Hoverbomb Gun and Bouncer are best for grouped tougher enemies like the v2.0 Megacorp Troopers ,and Megacorp Hover Tanks. Using other powerful upgraded weapons like the Megarocket Tube and Meteor Gun is also recommended if you need to.
At the start of the mission, cross a large bridge to reach a dead end. To proceed, you will need the Hypnomatic. Control a Receiver Bot on a nearby platform, and then use it to control a Receiver Bot on the platform to the left of that, passing on to others when the path is blocked by an impassable gap or force field, and deactivating any other force fields with switches. Eventually, you will reach a switch on the far right end guarded by v2.0 Megacorp Troopers; destroy them and activate the switch to conclude this section.
As Ratchet, use the Swingshot to access the platform in front of the compound, then destroy the Protopets and Megacorp Hover Tanks nearby. Then, head to the back, where there are two platforms leading to the main compound. Destroy the two Hover Tanks that appear, and then jump across the platforms to engage the large waves of enemies that will show up. While you cannot go through the main entrance, when the enemies stop appearing, a door on the far end on the left opens into another room.
You cannot cross, but must use the Hypnomatic to control a Receiver Bot. As this Receiver Bot, you will have to fight waves of Troopers and Protopets, but you have five more Receiver Bots you can control if your timer runs out. Defeat as many enemies as you can while avoiding damage, then when the time is almost up, switch to another Receiver Bot, until all enemies are defeated, and then stand on the switch in the door that opens on the end to open the main entrance. Head inside and use the teleporter to get in.
Use the Megacorp vendor to restock on ammunition when inside. At the end of the long corridor, you will be ambushed by Megacorp Troopers, then head down the corridor and head right to a platform in the middle. Destroy the Troopers that fly in on both sides, then continue forward to an area with blocks of cover which Troopers hide behind. These are best destroyed by sending blasts from the Hoverbomb Gun or Plasma Coil over it to destroy the Troopers until no more warp in. Another option is to get behind their cover and take out the first group, followed by catching each new group that spawns in off-guard.
In the next room, use the Dynamo to rotate the device in the middle, stand on it, and then jump across to the next platform. Kill the Troopers, then activate the Dynamo to jump across the next devices and then reach the end. In the next room, you will have to destroy all enemies before you can use the Infiltrator to open the door at the end. Once all are eliminated, use the Infiltrator to open the door behind it, kill the Protopets, then use well-timed double jumps to traverse the floating platforms to reach the opening at the end into another corridor.
Through the corridor, use the Swingshot across and then destroy the Hover Tanks located at the end of the room, then use the Swingshot again to reach the end and head right. Use the Electrolyzer to reactivate the large floating platform, stand on it to activate it, then jump across to the next room. Defeat all the enemies in here, then use the Swingshot to pull down the bridge at the end of the room. Defeat the final set of enemies that ambush you as you walk across the bridge, and a cutscene will commence. The mission is continued with "Defeat the mutated Protopet".