2+ save, and in cover

just a question that has been bothering me. Say a terminator is in cover, and you shoot him with an ap -3 weapon. Does he get a 4+ save, or a 5+ save? Im thinking it works like the 1+ saves that used to be in WHFB, but I wanted to make sure

A roll of a 1 is always a fail for a saving throw, regardless of whatever modifiers are applied, that is a rule.

In this system (I'm unfamiliar with WHFB) modifiers such as AP-3 and +1 cover are not applied to the save, but to the roll.

The Termi still has a 2+ save, but because you are subtracting 3 from the roll (AP-3), you actually need the D6 to display a 5+.

However, you are also adding 1 to the roll (cover) meaning you need a roll of 4+.

Just remember that modifiers are applied to the roll, not the save, and that they are applied simultaneously and you should be fine.