I don't know about 'ever', but Sin & Punisment for the N64 (Wii Virtual Console) immediately pops into mind. Probably because I just played it recently.

(SPOILER)The last boss is an artificial earth trying to destroy and replace the real earth. You have to defend the real earth from the artificial earth's various cataclysmic attacks and stuff while piloting an Eva. Pretty dern 'epic'.

If this were anime though (which it is not, but I like to pimp this show), there is no question that Tengen Toppa Gurren-Lagann is the most epic anime ever.