The plot is all over the place. The EDF stole the nanotech from Ultor, civil wars broke out on earth over the technology, nation states fought over the tech, Sopot and the Commonwealth were the last to get their hands on the nanotech. That raid was the introductory level in the game and the soldiers that would become Alias (the player) and Shrike were involved. Sopot used this technology to take over the world with Nanotech infused super soldiers, which he then turned on with more mindless creations that he could control. There were thousands of nanotech super soldiers that were mercilessly hunted down by Sopot's elite forces, now the remaining six are working with the effete Red Faction, and all of this information is conveyed via a cutscene after the intorductory level.
Red Faction 2 has completely broken away from the Half-Life styled presentation of the first game. You don't experience the majority of the story through the protagonists eyes, it's just fed to you through cutscenes. Volition did such a good job of making Ultor's security and mercenary forces out to be so cartoonishly evil in Red Faction. Like Snidely Whiplash mustache twistingly evil. Every time you round a corner an innocent miner or Red Faction insurgent is getting shot before your eyes. By the time you meet Capek, you're damned certain Ulto's main export is evil and mining is just a side gig. In Red Faction 2 you're simply told Sopot is evil and his regime must be toppled in a cutscene but you're never directly shown why.
When you kill Sopot, Molov (the leader of the nanotech super soldier squad) just steps in and becomes the next dictator, his first order of business is to kill the Red Faction (why are there martian insurgents on earth? Even if it's just a name it doesn't make any sense) and two of the nanotech super soldiers, Alias and I forget the name of the other one. "Ha ha, surprise, I am evil, this technology is mine!" You don't even care about the plot twist, none of the characters are likeable.
What's worse than having the game broken up by cutscenes and loading is that the loading mid-mission doesn't even make any sense for the vehicle sections. You'll be in a tank or jet, which is damaged, hit a loading screen and all of your vehicles health has been returned. It doesn't make any sense and removes pretty much and all challenge those sections might've had.
The nerfed destruction is the biggest crime. What you can destroy isn't even consistent, there isn't a visual logic to any of it. Some things can be blown apart, others can't be destroyed, some can only be destroyed after a scripted event. It's terrible. And the levels are so claustrophobic, you're literally just moving down a funnel.
Edit: 2.3 hours and I'm already halfway through the game according to
this FAQ
IV. Walkthrough
1. Foreign Lands
a. Complex Exterior
b. Containment Facility
2. Public Information Building
a. Lobby Level
b. Admin Area
c. Propoganda Studios
d. In the rain
e. To the Rooftop
3. Shrike's Wild Ride
a. Search and Destroy
b. Aerial Encounters
c. Brothers-in-arms
4. Underground
a. Alone in the Dark
b. The Train! The Train!
c. Rush Hour
d. The Bridge
5. Tank on the Town
a. Tank Gunner
b. Traffic Congestion
c. Road to the Citadel
6. Sopot's Citadel
a. Break in
b. Main Gate
c. Ammo Dump
d. Battle Armor
e. Hot Pursuit
f. Missle Silo
7. Hanging in the 'Hood
a. Mean Streets
b. High Rise Hell
c. Death from Above
d. High Rent District
e. In the back Alleys
8. Dancing with the Dead
a. Cemetery
b. Catacombs
c. Cathedral
9. A River Runs to it
a. On the Docks
b. Inside the Submarine
c. Dive! Dive! Dive!
d. The Right Way in
10. Inside the Nanobase
a. Industrial Processing
b. Repta Reunion
c. Having a Blast
d. No Place Like Home
e. The Nano Elite
f. Reprocessed
11. In Sopot's Deadly Embrace
a. Inside the Statue
b. Toward the Flame
c. The Final Battle