The dangerous Franks produced a stunning volley from the edge of the area to beat Morecambe keeper Barry Roche with virtually the last kick of the game.
Hartlepool had the better of the first half and Jack Baldwin headed them into the lead on 17 minutes when he raced into the penalty area to send a Matty Dolan corner past Roche.
The hosts then squandered a golden chance to equalise in injury time as Chris McCready missed an open goal when he headed wide from six yards out.
Morecambe, however, looked set to have sealed a point when Jack Sampson levelled the scores three minutes from time with an excellent left-foot volley that squirmed underneath visiting keeper Scott Flinders.
Both sides then went close to a winner in a mad final 60 seconds.
Franks hit the underside of the crossbar before the hosts broke away with Flinders redeeming himself for his earlier error with a superb double save to foil Sampson and the follow up from Kevin Ellison.
They proved particularly important when Franks popped up with his last-gasp winner.