(Synopsis taken from TFwiki.net)
Soundwave summons Megatron to the control room, saying that Laserbeak and Buzzsaw have detected massive energy readings underwater. The Decepticons investigate and encounter the Sub-Atlanticans, a race who hope to conquer the surface world one day. Megatron negotiates a deal with Nergill, King of Sub-Atlantica, offering Decepticon military technology in exchange for access to their geothermal storehouses. Starscream distrusts the Sub-Atlanticans, who communicate with each other telepathically.
Near the Autobot base, Spike, Bumblebee, and Hound are playing a game of football with the Dinobots. Wheeljack arrives before the Dinobots accidentally kill anyone, telling them there is a massive energy reading emanating from near the Decepticon base. Optimus Prime dispatches Bumblebee, Brawn, Hound, and Wheeljack to investigate, with Spike tagging along. The Decepticons and Sub-Atlanticans attack and take Wheeljack prisoner. After raising the city from the bottom of the ocean, the Decepticons and Sub-Atlanticans prepare to attack Washington, D.C. as a sign of their new alliance. Nergill communicates with his soldiers, telling Megatron that they will imprison Wheeljack in his dungeons. However, at Starscream's orders, Soundwave unscrambles the message and learns that Wheeljack is to be taken to their laboratory to develop weapons against the Autobots and Decepticons alike.
The Autobots head for Washington, hoping to stop the Decepticons and Sub-Atlanticans. Prime has Spike and Bumblebee head for Sub-Atlantica, hoping to rescue Wheeljack, while the Autobot leader takes the others to Washington. The Sub-Atlanticans raise a force field over Washington, trapping the Autobots inside. In Sub-Atlantica, Nergill has developed a magnetic dysfunction ray which will shut down Transformers; he's tested it on Wheeljack, leaving him immobile. Starscream discovers this and is shot by Nergill, who learns that it is less effective on Decepticons. As Nergill leaves, Starscream attempts to drain power from Wheeljack, but Bumblebee and Spike stop arrive just in time to stop the Decepticon and restore Wheeljack.
Nergill strolls into Washington, with Wheeljack, Bumblebee and Spike sneaking in behind him. Nergill uses the disruptor to defeat Prime's team of Autobots, bringing the battle to an end. As the Sub-Atlanticans secure the Capitol building, his soldiers ask when to move against the Decepticons, but Nergill decides to wait a little while longer. Meanwhile, Megatron (sitting at the Lincoln Memorial) tells Thundercracker that they will deal with the Sub-Atlanticans soon enough.
Wheeljack calls in the Dinobots, who manage to penetrate the force field and come to blows with the Decepticons. As Megatron and Grimlock grapple, Nergill is on the verge of shooting them both until Starscream arrives and bashes Nergill aside, declaring that he is now an enemy. Grimlock grabs the disruptor and destroys it, causing the Autobots to revive. The Decepticons and Sub-Atlanticans retreat back to their own city, with the Autobots in pursuit.
Back at Sub-Atlantica, Megatron demands an answer to Starscream's treason charge against Nergill, but Nergill informs him that the Autobots are coming. They invade the city, and the Dinobots begin smashing everything in sight.
Nergill decides to destroy the city, hoping to destroy the Transformers as well. Spike, Wheeljack, and Bumblebee follow, hoping to stop Nergill, with Rumble and Ravage in pursuit. The two Mini-Cassettes realize Nergill's intentions, and Rumble tries to bury him in rubble, but it's not enough. Wheeljack likewise tries to stop the sub-aquatic king, but it's too late. Nergill throws a device into his energy containers, which starts a chain reaction that begins to destroy the city. The Decepticons retreat; Prime orders the Autobots to clear out, then rescues Wheeljack's team (and strangely finds Grimlock there as well). Prime and the others escape, watching from the nearby sea as the Sub-Atlanticans and their home disappear under the waves. Prime says they probably won't see Nergill again for a long time.
Plot:

Not bad. Hey, let's get together with the sub Atlanticans and take over Washington DC. Nothing Earth shattering or revolutionary, but enough of a plot to keep the episode moving from start to end.
Animation:

Great annimation. Some of the best of season 2. Everything is clear and crisp, and the Transformers actually transfom as opposed to simply morphing into their modes.
Variety:

We get to meet a new race (albeit for this time only) the sub Atlanticans. We get to see the Dinobots playing football against some of the Autobos. Ths episode features 25 Transformers, Nergil, Spike, and he Sub Atlanticans. Although not quite perfectly accurate, it was cool to see scenes from Wasington DC. Seeing some of the episode take place underwater and parts on land was a nice bonus. Seeing Megatron sitting in President Lincoln's chair is classic.
Rewatchability:

Atlantis Arrise is one of my favorite eisodes. Clean plot with superb annimation is always a nice start. Throw in the dinobots and you've got a winner. I wouldn't have minded seeing Nergil make a reapperance later on, but unfortunantly this is his last apperance.
Best line:
Megatron - "You don't frighten me, you mechanical throwbacks!"
Grimlock - "Good, Megatron! We love stupid enemies!"