The infiltration of the Point Blanc campus by the SAS, meticulously coordinated, it nearly gets pulled off without any alarms being raised
Alex shooting a freaking snowmobile at a helicopter in Point Blanc.
Alex in a losing fight with Conrad, realises that all metal in him makes him Magnetic. He then punches him into a magnetic field.
Alex refusing to give Sarov the keycard for the nuclear bomb in the same chapter, even though he is being held at gunpoint.
Alex throughout Eagle Strike. Even when Alan Blunt burns him, Alex doesn't need official support and with only his housekeeper and some gadgets Smithers slipped him, picks apart Damian Cray's conspiracy in a few short days.
Alex on a tricked out bike against a hit team in several smart cars in a destructive chase through Ansterdam.
The fist fight between him and Damian Cray on a rapidly out of control Air Force One ranks as one of the series best fights
At the end of the book, for once, Alan Blunt gets dressed down by his bosses for not forseeing this crisis and is very nearly forced out of his position at MI6. After all the hell Alex went through during Eagle Strike, it's the best news he's heard during the series.
Nile's second meeting with Alex. He murders the man who discovered Alex in the pharmaceutical company hq, apologise for knocking Alex out earlier, leads him to a Alfa Romeo sports car, drives out of the complex and is zooming away just as the building explodes
The hot-air balloon scene from Scorpia in its entirety. Julia Rothman has unleashed a balloon with satellite dishes attached to it that will fire out beams which kill every schoolchild in London, and this includes Alex. So, he climbs up one of the ropes, and when he does get on the platform, he finds out that he can only knock out one of the satellites. It goes From Bad to Worse as Nile shows up and tries to kill Alex, with twin katanas. Alex then puts two and two together and realizes that Nile has a fear of heights, so he attempts to bring up that fear long enough to take one of his swords and cut the propane flow of the balloon, and it causes Nile to simultaneously fall to his death and burn alive. After this, Julia gets crushed by the balloon's platform, and Alex hitches a ride back to Chelsea on the hot-air balloon. To recap: Alex stopped a genocide-to-be and killed The Big Bad and her dragon with the use of a weapon that would have otherwise killed him... and then rode home using one of them. Fucking EPIC.
There's another scene with the SAS which plays parallel to the one above. At first, the Scorpia mooks are holding their ground, but then the SAS manage to turn the tide against their attackers despite being heavily outmanned and outgunned, eventually gaining the upper hand.
The badly humiliated Scorpia gets one at the beginning of Snakehead when they steal Royal Blue. In a surgical strike, they eliminate all perimeter security, gas the personnel inside and waltz in, easily taking the bomb and getting out with the British government none the wiser.
The introduction of Scorpia Rising where the leader of Scorpia heads to the British museum for a rendezvous. Predictably MI6 tries to rendition him. Unfortunately for the snatch team, Kurst's security detail slowly kills them off in a variety of inventive ways with the last one being run down by Kurst's bulletproof limo.
The entire chapter involving Scorpia's attempt to take down Smithers in Scorpia Rising.
Razim: ultimate Chessmaster. You have to give the guy credit for stringing together a plot to have the American Secretary of State assassinated in the midst of an anti-British speech by Julius, thereby linking Alex (who looks exactly like Julius) and the murder weapon with his fingerprints on it with the MI6. In Razim's eyes, this would destroy any trust that foreign nations have with Britain.
Alex executing Julius. It's tragic but after all the suffering he got put through, Julius misjudged Rider in the end.