The Bombers were blindsided when news broke that Merrett had met with Hawks coach Sam Mitchell just over three weeks ago.
Essendon have been adamant they won't let their captain, who is contracted until the end of 2027, leave the club.
There had been suggestions Merrett could skip Thursday night's club best-and-fairest event altogether, which would have humiliated the embattled Bombers, given he is expected to claim a sixth Crichton Medal.
But he was present with his wife Alexandra when Scott spoke to the room on Thursday night, including paying tribute to his skipper.
"Zach had another exceptional year and I know I speak for everyone when I say how proud we are to see him give his heart and soul for our club on a weekly basis," Scott said.
"It's been a difficult few weeks for Zach. It's been a difficult few weeks for Zach and his family, and I'd like to thank all those who have supported him
"We love you Zach. We love you and Alexandra and you'll always have my full support.
"Thanks for everything you've done."
Scott, who had his right arm in a sling, also flagged the Bombers will host Hawthorn in round one next year.
Merrett was already out to a commanding lead in the best-and-fairest count by round nine of the count.
Earlier Merrett chose not to speak to reporters when approached on his way into the event at the Centrepiece function centre.
"I've already covered this at the Brownlow," he said.
Merrett was at a table that included departing defender and close friend Jayden Laverde, on-baller Jye Caldwell, forward Matt Guelfi, midfielder Will Setterfield and young gun Nate Caddy.
Senior players including Andrew McGrath, Kyle Langford and Nic Martin were on different but adjoining tables to the skipper - whose captaincy appears untenable if he does ultimately stay.
New club president Andrew Welsh didn't address the elephant in the room in his speech, but attempted to galvanise the crowd.
"I'm all about one Essendon, one club," he said.
"My message applies to everyone in this room, from our players, coaches, staff and volunteers to our members and supporters.
"This is our time to galvanise. Our foundations are set and it's time to unite.
"We win together, we lose together. But we stick together - and when we stick together, we're a formidable club. All in, all heart.
"This is our time, this is our moment and we're about to embark on our greatest era yet, so let's get running. Go Bombers."
The Bombers haven't tasted premiership success since 2000, and last won a final in 2004.
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