The IPCA mostly survived intact - but Lian Xing was wounded and Imani Grey killed in an aeroplane crash. Murukawa Industries was utterly destroyed in a C4 explosion which the agents triggered - along with the demise of Iwao Ryusaki, numerous Yakuza officers and a substantial amount of tower security personnel. Korin Matsua and innumerable HNT thugs were also killed in action.
Having been a secretary in the building beforehand, Lian had secured a general layout, and reported the presence of numerous restricted areas with increased security. She used contacts in the Japanese underworld to persuade the HNT that Murukawa was attacking them, thus instigating a turf war between the Yakuza and HNT, believing this would immensely aid the IPCA in recovering the gangster boss alive for questioning.
"Gina, gather the team and get going. Be careful! You're the last pilot we've got. I want 'em in Tokyo by tonight."
"Yes, ma'am. Leaving now. Come on, hotshot. Let's not keep the lady waiting."
With the Lorelei permanently vaporised and remaining samples of Syphon Filter destroyed, Lian reports that Imani is following Yong-jun Kim; both flew out from Tokyo. Gabe and Gary Stoneman were both still in Moscow, so the IPCA commander did not learn of Crusher's demise. Despite their losses, Lian ordered Gina to bring the team to Tokyo, and told them to exercise extreme caution.
"ETA to Murukawa Tower is 0-0-2 minutes."
"Alright, this is a shake and bake op with 4 goals. First, find Murukawa. Our primary goal is to get in, take him and get out. Second, take out Murukawa's labs. Your loadout has enough C4 to take out the entire floor. Next, DPE's. I have one for each of Murukawa's officers, and one for the HNT leader, Korin Matsua."
"That's our cue."
"Hot LZ. HOT LZ! HANG ON!"
"Teresa, we're going down! Say again, our LZ is hot! We're going down!"
"Come on! COME ON! Get up there!"
As the copter approaches their insertion point, Lian briefs the operatives on their tasks. They arrive at the helipad, but Murukawa's thugs are waiting, and fire a missile at them. Gina Hunter barely manages to bring the copter to a landing on the streets.
Protecting the copter
"One of the stabiliser controls've been hit, I'm gonna need a minute to fix it."
"You heard the lady, buy us some time to get this bird in the air."
As the IPCA agents deploy, they come under fire from Japanese goons. They provide cover for Gina and Lian while the stabiliser controls are repaired.
Neutralising Yakuza officers (outside the tower)
As the copter flies off, Lian and Gina head to LZ1 for more repairs. The agents head for the Murukawa tower, and are assaulted by Yakuza officers who they need to neutralise. Before infiltrating the tower, they eliminate the first group they encounter.
Neutralising Korin Matsua
As they head into the garage, the agents run into Korin Matsua, one of the bloodiest criminals whom Lian had ever encountered. They engage him in a firefight and take him out.
Neutralising Iwao Ryusaki
Upon infiltrating the building, the agents come across Iwao Ryusaki, Murukawa's security commander. Using his immobility against him, they defeat him and recover the elevator control panel.
Neutralising Yakuza officers (inside the tower)
Now able to access the upper levels, the agents continue taking out the Yakuza officers in the building.
With the fifth floor containing a security panel, the operatives employ stealth and guile to bypass the patrols. This allows them to access the more secure levels top floors.
Uploading computer information
"That's the central information data centre. Find the main terminal and start uploading data."
The team reaches floor six, which contains a computer, and upload the intel from the database.
Search for the surveillance tape
"Teresa, Murukawa's dead. Looks like a suicide."
"I'm guessing that'll make it hard to interrogate him."
"Huh. You're a big help."
"Sorry. Still trying to get used to this 'chief of operations' thing."
When they reach Murukawa's office, the agents find him dead and attempt to locate the video tape from Lian's planted camera to find out what happened.
Securing the LZ
"Gina, the rooftop's been cleared. Get ready to take off."
"Copy that, we're ready to go."
The team head to the helipad and clear it of enemies. With the area safe, Lian tells Gina to take off, their next destination being the tower.
Infiltrating the labs
"This must be Murukawa's lab. There'll be a self-contained viral holding unit somewhere in here. Elsa wants us to get samples if possible but I told her that wasn't our top priority."
"Lian, warn 'em to put on a HAZMAT suit before they enter the protected area of the lab. Otherwise they're gonna risk contamination."
"Copy that. The lab's schematics show that the HAZMAT suits are stored near the decontamination airlocks."
Inside the labs, the team acquires a sample of the virus Murukawa kept somewhere, and deploy C4 charges in the general area.
Falling back to the roof
"LZ achieved, repeat, we're at the LZ. Your ride is here, let's move!"
With their tasks largely complete, the operatives head to the roof, where the copter lands. They fend off an incoming wave of more hostiles before leaving.
"Murukawa Industries is out of business."
"Teresa, Lian's been hit."
"It's nothing. Mission accomplished... but... we didn't get Murukawa. Tell Gabe-"
"Wait, I've got news! It's not good..."
"Imani's flight. It's just gone down."
"What d'you mean?"
"She's gone, Lian. No survivors."
"Take us home, Gina."
Despite having accomplished most of their mission, Lian regrets the loss of Murukawa. Teresa reports more bad news: Imani's flight went down without survivors. Guilt-stricken, Lian tells Gina to bring them home, for an unsanctioned operation she has in mind: to retrieve her colleague's remains.