On August 12, 2011, large masses thought to be meteors land in the oceans near several major coastal cities. The objects are discovered to be spacecraft containing hostile extraterrestrial life. Marines from Camp Pendleton arrive in Los Angeles, including SSgt. Michael Nantz (Eckhart), an Iraq War veteran. Nantz was to begin retirement, but because of the attack, he is made the acting platoon sergeant for 1st Platoon, Echo Company, of the 2nd Battalion 5th Marines.
Under the command of 2ndLt William Martinez (RodrĂ­guez), the platoon arrives at Santa Monica Airport, now a Forward Operating Base. The alien ground forces have no apparent air support, so the Air Force prepares to carpet bomb the Santa Monica area, and the platoon is tasked with rescuing civilians from an LAPD police station in West Los Angeles before the bombing. As they advance through the city, they are ambushed and suffer multiple casualties, namely Grayston, Guerrero and Lenihan in the firefight. Nantz takes Imlay and Harris to look for Lenihan, who is missing from the group after having been wounded. After fighting off a hostile alien, they manage to regroup and team up with a group of Army National Guard soldiers from the 40th Infantry Division, and an Air Force intelligence TSgt, Elena Santos (Michelle Rodriguez). At the police station, the platoon finds five civilians: veterinarian Michele (Moynahan), children Hector Rincon (Cass), Kirsten (King) Amy (Gould), and Hector's father Joe (PeĂąa). A helicopter arrives to evacuate the wounded Marines, but cannot rescue the civilians due to weight restrictions. As the helicopter takes off, it is destroyed by alien air forces, killing Grayston, Guerrero, Lenihan and Simmons.
The Marines commandeer a city bus for evacuation. They also vivisect a wounded alien with the help of Santos and find a vulnerable spot in its torso, as well as learning that the alien aircraft are drones that track down humans through radio transmissions. Santos reveals that her original mission was to locate the aliens' central command center, believing that its destruction would deactivate the drones. On the I-10 freeway, the bus comes under attack. Because the off-ramp is destroyed, the Marines are forced to rappel the civilians off the freeway. Marines Stavrou (Pesi) and Mottola (Liao) and the National Guard soldiers are killed, while Joe and Lieutenant Martinez are wounded. Martinez detonates explosives inside the bus, killing himself and the aliens, leaving Nantz in command. The surviving Marines Nantz, Santos, Imlay, Kerns, Lockett, Harris, Adukwu and the civilians escape the bombing zone. A news report speculates that the aliens are seeking Earth's water for fuel while attempting to colonize the planet and eradicate humans. The team prepares for the bombing, but nothing happens. Returning to the FOB, the Marines find that it is destroyed and the military is retreating from Los Angeles. The Marines plan to escort the civilians to an alternate extraction point. Joe dies from his wounds and Lockett confronts Nantz over his brother, Cpl Dwayne G. Lockett and the others who were killed in Nantz's last tour. They come to peace when Nantz explains that he thinks of them every day, and recites each person's name, rank and serial number. Nantz then says that the surviving Marines should move forward united to honor their fallen comrades, including Joe. They successfully reach the extraction point and evacuate through a helicopter.
In mid-air, the chopper experiences a brief loss of power. Nantz theorizes that they are hovering over a location occupied by the alien command center as it relays radio energy to its drones. He decides to recon the area alone, but his team insists on accompanying him. Searching underground, the Marines confirm the presence of a large alien vessel. Kerns radios in to request for missiles, which Nantz manually directs using a laser designator while the others defend his position. Despite Kerns being killed when a Drone spots his signals, the Marines succeed in routing a missile to the command module, which is destroyed. The alien ground forces retreat as their uncontrolled drones crash, just as reinforcements for the Marines arrive. At a Temporary Operating Base in the Mojave Desert, Nantz, Imlay, Lockett, Harris, and Adukwu, the six survivors of the original platoon along with Santos, are greeted as heroes. Despite orders to rest, they re- arm themselves and join the rest of the Marines in retaking Los Angeles as other countries wage similar military operations against the hostile species.

Question: What do the marines confirm the presence of after searching underground?
Answer: large alien vessel
Alternative answer: The alien command center