Unlike the previous GBA installment, this one is more polished and incorporates stealth better. It even has some of the trial-and-error feel of the console versions. This game has a habit of slapping you with "MISSION FAILED" if you run around killing enemies mindlessly. Strangely, enemies have slow reaction so it is easy to run up and grab someone from behind, and there still are ways to hide from SWAT guards if you set off an alarm (but not fail).
The fastest way to terminate an enemy is to drop from a height onto him. Next fastest is to shoot him. Unlike the previous, some enemies take more than one head shot to kill. When firing, wobbling cancels gun animations. It is possible to use friendly fire to take down enemies. Failing that (or when not allowed), it is possible to melee some enemies, or grab them from behind and knock them out, but it takes a long time.
Although guards may detect something is behind them, their reaction is so bad that you can usually grab them anyway, so it doesn't matter if you run behind them.
There are a few ways to set off alarms in this game:
- Let any enemy run to an alarm panel and use it.
- Walk in view of a camera (the sticky cam view shows the camera's view).
- Touch any infrared lasers (the base of the lasers is visible; the thermal vision shows the lasers).
- Let any spotlight see you.
- Let any "window guards" see you.
- Let any camera see a body.
- Let any enemy see a body and run to an alarm panel and use it.
- Exit a room with a conscious enemy around which saw you (except special event).
- Exit a room when a camera can see a body (except special event).
- Exit a room when any enemy can see a body (except special event).
There is also a scripted alarm late in the game.
When an alarm goes off, either the mission fails or SWAT guys run around. These guys are hard to terminate and spawn every time I enter a new room so I don't just go around setting off alarms.
Health is very important. Sam has 10HP maximum. There are some health refills, and they do not take as long to use as in the first game. Here is a list of what causes damage to Sam:
- Weak embassy guards: 1 damage
- Ground turrets: 1 damage (ignores recovery)
- Guards during sniper minigame: 1 damage (ignores recovery)
- Blue guards: 1 damage
- Yellow guards: 2 damage
- Mini SWAT guards: 2 damage
- Jerusalem police: 2 damage (melee does 1 damage)
- Firebombers: 3 damage (kick does 2 damage)
- Flamethrowers: 3 damage
- Assault rifle guards: 3 damage
- Alarm SWAT guards: 3 damage
- Wall turrets: 3 damage
- Mine explosions: 3 damage
- Damaging fall: 3 damage
- Falling off the bottom of the screen: instakill
If a damaging fall occurs, a landing animation is forced where Sam cannot move, wasting time. I never use damaging falls in this run.
Here is what damage Sam can cause to enemies:
| Enemy (6HP) | Head shot | Low shot | Melee | Kill | KO |
| Civilians | 6 | 6 | 6 | - | 1 melee |
| Embassy guards | 6 | 6 | 3 | 1 head shot | 2 melees |
| Blue guards | 6 | 3 | 3 | 1 head shot | 2 melees |
| Yellow guards | 6 | 3 | 2 | 1 head shot | 3 melees |
| Jerusalem police | 3 | 2 | 1 | 2 head shots | 1 head shot, 1 low shot, 1 melee |
| Firebombers | 6 | 2 | 2 | 1 head shot | 2 low shots, 1 melee |
| Mini SWAT guards | 3 | 0 | 2 | 2 head shots | 3 melees |
| Assault guards | 3 | 0 | 2 | 2 head shots | 3 melees |
| SWAT guards | 2 | 0 | 0 | 3 head shots | - |
For those who care, here are the stats given by the game at the end of each level:
| level | time | bullets | alarms | KOs | kills |
| Embassy 1 | 5:44 | 7 | 0 | 37 | 0 |
| Embassy 2 | 4:15 | 17 | 0 | 26 | 9 |
| Subway | 3:06 | 33 | 1 | 1 | 21 |
| Saulnier | 6:08 | 31 | 7 | 17 | 35 |
| Jerusalem | 1:38 | 14 | 0 | 8 | 3 |
| Warehouse | 7:24 | 37 | 0 | 14 | 1 |
| Shipyard | 8:36 | 70 | 6 | 10 | 62 |
| Submarine | 1:33 | 19 | 3 | 11 | 8 |
| TV Station | 3:48 | 52 | 6 | 6 | 30 |
Bold means that alarm = mission failure.
Note that the times do not count when dialogs and "It's not time for this now" glitches are active. For example, by careful use of the glitch, one can obtain "impossible" stats for the Jerusalem level as in the image on the right like I did once (unassisted). The actual time was significantly longer than the actual time in the TAS.