The last time Lynch saddled a runner at Flemington was in the 2014 Bagot Handicap when Callmedan finished seventh.
Alainge gave Lynch his biggest victory in 15 years of training when successful in the Listed Port Adelaide Cup at Morphettville on May 2.
Lynch began thinking about Saturday's race after Alainge finished fifth in the Adelaide Cup (3200m) at Morphettville in March.
"She ran a really good race in the Adelaide Cup and was just way too far back and finished off really strongly," Lynch said.
"After getting the two miles for the first time, I thought we'd head down this direction and try and qualify for the Melbourne Cup.
"Ask any trainer, and their aim is to win the Melbourne Cup, and I'm no different."
Lynch said he had only previously had two runners at headquarters and that Alainge was his best chance, 'by far'.
"My early training career, I was only 23 or 24 when I had my other Flemington runners," Lynch said.
"My last runner was seventh in the Bagot.
"Back then I was based at Murray Bridge but every summer I would base myself at Cranbourne for three or four months and I did that for about four years then."