- Fall of Cerberus Base
- With the location of Cronos station finally exposed, Shepard and company set off (possibly with the help of STG) aboard the Shadow Base. When the base exits its mass effect corridor onto its destination, it is to find a large cylindrical base, far larger than the Shadow Base, hovering in deep space. The base is not located near any sun.
- Instantly Cronos opens fire on the Normandy, Shadow Base, and other vessels and kodiaks that Liara is commanding. Shepard and his squad leap aboard their kodiak and fly through the deep space fray towards the seeled entry way of a large shuttle bay. EDI, Kasumi (if alive), and Glyph hack Cerberus's security, allowing the assaulting kodiaks to fly through the bay doors.
- They land in the chaotic shuttle bay of Cerberus. Shadow Broker troops and Cerberus terrorists are in full combat already. Jumping off the kodiak, Shepard and company scramble for cover. Shepard spots Kai Leng upon a high balcony, firing grenades down at Shadow Broker troops. Leng catches sight of the commander, and launches a grenade which explodes against crates Shepard was trying to use for cover. The squad is knocked over and stunned, while high upon the balcony, Leng prepares a killshot. Just in time, a random rocket (presumably fired by a Shadow Broker mercenary) strikes the supports of the balcony Leng stands upon. The assassin's shot goes wide, and he falls out of sight.
- One of Shepard's squadmates recovers, and staggers to their feet, only to see Leng sprinting through the chaos towards them. Before they can target him, the assassin, leaping acrobatically over shuttle bay wreckage, punts the squadmate in the head with his powerful mechanical legs. Clearly only seeking to provoke Shepard, Leng darts away through a door and disappears.
- If the squad mate punted was Ezno, Jack, or Aria (temp), they will recover, their face covered in blood, and enraged pursue Leng through the fray. Shepard reigns them back under control through various paragon, renegade, responses.
- If the squad mate punted was not Ezno, Jack, or Aria, they will be dazed and bloodied, but otherwise alright. Later, back aboard the Normandy's medical bay, it will be revealed that they suffered a minor concussion.
- If the squat mate punted was Wrex, Grunt, or EDI, they will recover easily, scoffing and Leng's provocation.
- Shepard and his squad help the Shadow Broker mercs (and STG agents, if recruited) secure the shuttle bay, while EDI hacks the door Leng escaped into.
- If Legion was sold to Cerberus in ME2, before Shepard and his squad can pursue the assassin, Legion appears on another balcony high above the fighting, and starts sniping Liara's mercenaries below. Legion is a boss fight. After the Cerberus controlled geth platform is defeated, it falls from the high place, smashing against the shuttle bay floor, destroyed.
- With the bay more secure, Shepard and company refocus on pursuing Leng by going through the door (now accessible thanks to EDI) that the assassin escaped through.
- Shepard chases Leng throughout the base. Leng tries several times to lead Shepard into rooms where he can set up an effective trap, but EDI, doing a thorough scan of the base is able to close these doors before the assassin can utilize them. With his pathways being funneled by EDI, Leng makes his way towards what EDI believes is TIM's office – though nobody is surrprised by this.
- Leng finally comes to a halt in a wide room with an elevator. Cerberus troops shoot at Shepard and company before they can comfront Leng, and the Normandy's crew ducks for cover, while Leng waits for the descending elevator.
- If Shepard is a Vanguard, the commander leaps out from behind cover, and bullrushes the Cerberus mercenaries, smashing them with biotic charges, punches, and nova strikes. Leng, momentarily stumped by this show of carnage, ducks inside the arrived elevator, and manages to close the doors, just as Shepard performs a final biotic charge at him. The elevator is rocked as the force of Shepard's biotics slam into it, and the door is dented. Leng escapes. Shepard's squadmates are in awe.
- If Shepard is a Sentinal, the Commander leaps out from behind cover, activates tech armor, and advancing slowly, mows down Cerberus' mercenaries with gun fire, tech skills, and biotics. The mercenaries are unable to penetrate Shepard's armor, and Leng scrambles behind one of his troops, using her as a human shield. The elevator opens, and the assassin ducks inside. Before the doors can close, a final biotic attack from Shepard sends the final merc flying into the compartment, knocking Leng over. Leng escapes. Shepard's squadmates are in awe.
- After these troops are defeated and Leng escapes, a small handful of Shadow Broker troops, tired but hardy meet up with Shepard. Shepard is intent on following Leng, but the SB troops say that there are incoming Cerberus mercenaries chasing them. Not wanting to risk letting the assassin escape with TIM, Shepard chooses a squadmate to help down the room, and calls the elevator. EDI scans the elevator, noting that its security camera showed Leng leaving the compartment without planting a trap in it.
- Shepard and his remaining squadmate take the elevator up to the top floor to TIM's office. TIM's office is empty, except for the sillhouette of Leng, who is looking around, slightly confused. Shepard asks where TIM is. Leng shrugs, challenges Shepard to a fight, and no matter how the Commander responds, the assassin charges. Leng is armed with a cloaking device, his combat knife, and a grenade launcher, and of course his powerful CQC kicks.
- If the Collector Base was destroyed, there are also TIM's two Cerberus Hound mercenaries, flanking Leng. As extremely talented shocktroopers, they are armed with heavy assault rifles, extreme agility, and biotics, making these shocktroops bolster the difficulty of the boss fight.
- Once defeated, Leng slumps to the floor of TIM's office, mortally wounded.
- If Shepard is a Vanguard/Adapt, the Commander can grab Leng and use biotic punches to reduce Leng's head into a bloody stump. Renegade prompts allow Shepard to recite the names of his murdered comrads as he strikes Leng.
- If Shepard is a Soldier/Infiltrator, the Commander can grab Leng and stab him in the stomach, causing Leng to cough up blood. Renegade prompts allow Shepard to recite the names of his murdered comrads as he strikes Leng.
- If Shepad is an Engineer/Sentinal, the Commander can grab Leng and, activating Shepard's omni gauntlet, electrocute the assassin. Renegade prompts allow Shepard to recite the names of his murdered comrads as he strikes Leng.
- If Shepard takes the paragon prompt, he can attempt to heal Leng with medi-gel. The assassin quickly crawls away from Shepard, cursing him for his weak resolve, and finally bleeds out.
- Alternatively, if Shepard has Aria, Ezno, or Jack as his squadmate for this section, the Commander can let them kill Leng by punching him to death.
- The assassin succumbs to his injuries, and Shepard snatches the N7 dog tags back from Leng's chest.
- With Leng dead, Shepard and company turn their attention towards what remains of TIM's office. The Commander goes to TIM's desktop console, and with EDI's hacking skills, gains control of the base. Shepard tells the remaining Cerberus troops to stand down, shuts off the bases defenses, and has the option of turning on the office's lights. Shepard turns on the office lights, the sun hologram and constilations display deactivates, revealing an unimpressive black room with a secret door in a corner. EDI informs Shepard that TIM has likely escaped through the passageway behind the door, which leads to an escape pod bay.
- Shepard and his squad charge after TIM, hoping to find him before he can escape. TIM's voice comes in over the intercom, scoulding Shepard for the destruction of the base, and jeering at Shepard's inability to capture him. Shepard manages to reach the escape pods, but they are already being launched, and the Commander watches helplessly as TIM's pod rockets off into space... only to crash, almost comically, inside the the docking bay of the Shadow Base. Liara, anticipating TIM's flight, managed to locate the escape pods on Cronos station, and purposely caught TIM's pod before it could make an FTL jump.
- The Fate of Cerberus
- Shepard returns to TIM's office, and recieves a call from Liara. T'Soni wishes for Shepard to use EDI to transfer the data in Cronos Station to the Shadow Base so that she could expand her empire. Surviving characters will chip in, attempting to halt Shepard's decision in order to forward their own interests.
- Miranda wishes for Shepard to retain Cerberus's data, believing that she could effectively run Cronos station, and (inspired by Liara) turn the terrorist cell into something better. She suggests that Shepard and Jacob join her in this operation. This choice allows for Miranda to aid many remote human colonies struggling to fight off husk forces.
- Jack wishes for Shepard to destroy the base to show the Council that he is not aligned with Cerberus's ideals, and because of all the pain and suffering Cerberus caused in the past. This choice works well for Shepard in his trial, because it shows the Commander's willingness to turn from power.
- Ashley/Kaidan wishes for Shepard to transfer Cerberus's significant funds and data over to the Alliance, strengthening their political and physical power. With the Alliance strengthened significantly, they would be able to better fight the war effort, save lives on Earth, and get a stronger foothold in the galactic community. This choice works well in influencing the human Council member(s) and giving humanity extra political power (via data, manipulation) on the Citadel.
- Shepard makes his decision, and leaves the base.
- Back aboard the Shadow Base, Shepard and Liara approach TIM's crahsed pod, whose collision caused a fire in the docking bay. When the fire is put out, they crack open the escape pod's door.
- If the Collector Base was destroyed in ME2, TIM is found dazed and bruised inside. Shadow Broker mercenaries quickly arrest him, and drag him off to a cell.
- If the Collector Base was captured in ME2, TIM is not inside the pod. Shepard and Liara realize that TIM must have abandoned Cronos Station for the Collector Base prior to their assault.