Blowfish is a daemon which raises the alarm tracker by 1–3 steps; the number of steps is random. If this advances the alarm tracker to the next alarm level, then any effects of raising the alarm level will be triggered immediately.
Blowfish 2.0 is an archdaemon which can occur from mission difficulty 5 and onwards in Endless modes. It raises the alarm tracker by 10 steps at the start of the mission, so that the mission starts at alarm level 2. All effects of raising the alarm level will be triggered at the start of the mission.
Raising the alarm tracker brings additional security measures sooner. Be particularly careful if this could happen during your turn, especially if a new guard will arrive — normally this would happen at the end of the enemy turn, so the guard will not move until a turn later, but if a guard arrives on your turn then they won't wait in the guard entrance for their turn.
If you are in a position to wait a couple of turns to avoid triggering Blowfish, this is usually the right thing to do. Maybe you can wait for enough PWR to use Hunter or Taurus, or to use an EMP Pack instead of hacking. The alarm tracker will rise the same amount if you wait 1–3 turns or trigger Blowfish, but if you wait then you can do other things during those turns too.
If the alarm level has already reached 6, then there is no downside to triggering Blowfish unless there is still a Scanning Amp or Router which you have not disabled. After alarm level 6, Blowfish can be strictly good for the player because of the uncapped bonuses from Network Siphon and Reactive Myomer.
The Blowfish 2.0 archdaemon in Endless modes makes Rapier and Gel Injectors much less useful. On the other hand, Dynamo will generate PWR from the start of a Blowfish 2.0 mission.