Zed makes a stunning announcement: He's retiring; he's decided he's too old and weary to lead MiB into the next century. Kay will be his replacement, Jay will get a new partner. Zed is given a retirement party, neuralized and immediately "re-located" to pursue a new life fishing on Long Island. But it seems Zed's timing couldn't be worse: Alpha is back, is up to something big and must be stopped. With Kay promoted to chief, Jay is eager to get himself a new junior partner he can boss around. But his bubble is burst when he's assigned a new partner - Elle. Out in the field, Elle and Jay locate Alpha, who sports formidable new body parts and powers. Jay gets captured. Alpha tortures and brain probes Jay, who finally "breaks", revealing to Alpha where Zed has been re-located to. After Alpha takes off in pursuit of Zed, Elle rescues Jay and lets him know the truth: Zed was never really retired or neuralized. It was all a ruse, part of a sting operation to draw Alpha out into the open, where he could be ambushed by MiB agents. Jay was kept in the dark, so that when he was captured by Alpha (which Elle helped orchestrate) the brain probe wouldn't give the plan away. As Jay stews over being used both as a patsy and as bait, they arrive on Long Island to discover that the sting has gone awry: Alpha figured it out, and has gotten the drop on the MiB ambush. In an action-packed climax set on the dune-filled beach, Jay redeems his wounded pride, and Zed proves he's anything but over the hill, when they team up to destroy Alpha ... who in the end reverts to his human form and is put away for good.