Activating the Declassified Mission Skull upstairs will make nemacysts attack the beacon. This will make escorting and protecting it a bit tougher. Clear the enemies in the next room the enter the burning room ahead. You should spot the COG Tag Skull. Enter the next room through the burning hole and find the COG tag in the corner of the room, behind the tables.
Continue to the barred door and take cover as the bot cuts it open. More enemies will arrive from one side of the room. After taking them out, nemacysts will arrive from the opening on the ceiling. If you have the declassify mission active, they'll all be heading towards the bot.
Once the door's open, head outside. Continue following the bot until it freezes and sounds an alarm. Stay close to it and fire at the attacking nemacysts. Fire short, controlled bursts and perform active reloads to ensure that none of the nemacysts will go through. Move ahead until the bot stops again in a tunnel. More enemies will appear where you came from and heavy enemies will emerge on the area upstairs. Guard both sides, especially when the nemacysts appear.
Once the enemies are taken care of, regroup with your team to complete the section.