Which is the correct punctuation?

I would prefer the second.

Many thanks, Setanta!

I think there should be a comma before and after the and. However, I think the first way is preferable.

Why not just replace the word "and" with a period?

Once more unto the breach.

The correct punctuation allows you to move or remove phrases without the sentence losing sense:

1. Our immune system is constantly on the lookout for invaders, and once an enemy is spotted, (our immune system) mounts a complex attack.

Our immune system is constantly on the lookout for invaders, (our immune system) mounts a complex attack, and once an enemy is spotted.

Incorrect.

2 .Our immune system is constantly on the lookout for invaders and, once an enemy is spotted, (our immune system) mounts a complex attack.

Our immune system is constantly on the lookout for invaders and, (our immune system) mounts a complex attack, once an enemy is spotted.

Correct.

Delete the repetition shown in brackets.

The use of commas in the sentence is optional, bordering on superfluous.

Our immune system is constantly on the lookout for invaders, and mounts a complex attack when an enemy is spotted.

Thanks to all those who replied, especially to Miss Toad for her analytical reply!