G.I. JOE AND THE TRANSFORMERS issue #2 was printed on November 4, 1986, two months after issue #1, with a pull date of December 1986.  The issue is entitled "Power Struggle" and is from the same team as issue #1—Michael Higgins as writer, Herb Trimpe on pencils, Vince Colletta inking the art, Joe Rosen as letterer, and Nel Yomtov coloring the art.

The front cover showcases the Decepticons (Shockwave, Dirge, Bombshell, and Ravage, who should be dead) watching a monitor showing some sort of battle with Cobra and G.I. Joe forces, while numerous people in bikinis and swim wear run for cover.  The Decepticons surrounding the view screen are painted entirely red, and it creates an eerie atmosphere, like they're watching from the depths of a submarine or something.  

Bob Budiansky had previously written Ravage out of the comic book in isue #20, though, so his appearance here is erroneous.  Ravage disappears again after this story, incidentally.

The story picks up where the last issue left off, with Superion arriving and demanding to know what's become of poor Bumblebee.  The Joes are awe-striken at his sheer size, and I honestly wonder if perhaps he's drawn a little TOO big?  Superion never really interacted with humans until this story, so I've never gotten a clear sense of scale.  But, if we put aside the fact that they're all jets, and assume that Superion is the same size as Menasor, then Superion's arms should only be the size of cars.  Which means he's at least twice as big as he should be in this story.

Scarlett sounds the alarm, and the Joes rally to mount a counteroffensive.  Superion fires several warning shots, making clear his intent not to hurt anyone.  When the Joe firepower gets hot and heavy, though, Superion seems to be weighing his choices—allow them to destroy him, or kill them all to preserve himself?  Just then, however, he is alerted to the news of Optimus Prime's destruction, and Blaster immediately recalls him to the Ark.  So, these events must be taking place just after TRANSFORMERS #24.  Superion launches into the sky and withdraws.

A couple of artwork oddities here.  For one, Blaster is being colored like Optimus Prime for some reason.  Even stranger than that, though, is that Blaster sports an alternate character design, one more in synch with his Sunbow cartoon appearance.  But, this is not how Blaster normally appears.  In every Marvel issue up to this point (except his TRANSFORMERS UNIVERSE profile), he's been drawn more like the toy, with a Batman mask covering his eyes.  Somebody didn't communicate to the art team for this mini-series that Marvel's version of Blaster doesn't look like the cartoon Blaster.

In the aftermath, Mainframe (the Joe computer expert who makes his first Marvel appearance here) is examining what remains of Bumblebee to try to understand the robots better.  "There's more to this picture than meets the eye," he says, cheekily quoting the familiar Hasbro jingle, "but all I have here are a few pieces of what seems to be a rather beat-up Volkswagen."  Also, General Hawk takes the time to visit Senator Larkin at Fort Lewis to offer her some companionship after the recent terrifying events.  She locks the door, and the close-up of the doorknob is understood to be universal code for the two about to get jiggy with it.

It's 1986, and the Transformers have been active on Earth for two years, and yet the Joes are still acting like they've never heard of gigantic transforming robots from outer space.  Maybe the higher-ups have designated all information about the robot threat as classified, so the enlisted officers just aren't told about it.  That's certainly possible.  

At the Decepticon base, Megatron is in a serious funk.  Shockwave and Ravage are trying to cheer him up—Optimus Prime has been destroyed, after all.  But Megatron is lost in his own little world, saying things like "the road to my destruction is already paved."  Under normal circumstances, I would say this is highly out of character for Megatron.  But, we'll see in TRANSFORMERS #25 that this is pretty consistent with his depiction in that issue, albeit in a different writing style.  This issue is forecasting his imminent destruction in a way that TRANSFORMERS #25 did not; in that issue, he's just haunted by the ghost of Optimus Prime, but in this story he's acting like he's already given up on life.  It's hard to reconcile the two approaches.

Also, it doesn't make sense that Megatron is already at the new Decepticon base in the Florida Keys.  In TRANSFORMERS #25, the other Decepticons were being transported there one at a time by Vortex, while Megatron was tangling with Predaking.  He ended up blowing up the space bridge shortly thereafter.  There simply wasn't time for him to go to the new base and mope around.

On Cobra Island, Dr. Mindbender notices that Power Station Alpha has activated itself, thanks to the cerebro-shell that Bombshell had implanted in the previous issue.  The power station blasts off, and even interrupts Hawk and the Senator's smooch session.  Also, it's weird to me that Hawk is blonde in the comics.  I'm used to him having brown hair, as per the cartoon series.  As a blonde, he looks too much like Duke to my eyes.  Anyway, Mindbender puts on a control helmet and attempts to electronically sieze control of the power station.

Elsewhere, Tony Duranti and his mom are back at home, but he's still seemingly in a state of shock.  He's still completely out to lunch, as a result of being manipulated by Bombshell's cerebro-shell.  He's also toting around a Bumblebee toy, weirdly enough.  The main G.I. JOE comic has made cheeky references to Transformers in previous issues.  G.I. JOE: SPECIAL MISSIONS issue #5, for example, from June 1987, has Slip-Stream showing off a Transformers toy he's bought, Jetfire, and marvels at how it transforms into a swing-wing fighter jet.  (They actually show a tiny Megatron toy, not Jetfire, but that's neither here nor there.)  G.I. Joe writer Larry Hama didn't like the idea of there being a shared universe, and seemed to go out of his way to establish Transformers as fictional characters within his G.I. Joe universe.  The appearance of the Jetfire toy takes place after the G.I. JOE AND THE TRANSFORMERS crossover (which Hama did not pen), suggesting an intended retcon.  Of course, real live Transformers characters would eventually show up in the pages of G.I. JOE proper, but not until about issue #142, nearly eight years later.  

A Cobra fleet of Rattlers accompanies Power Station Alpha towards its new destonation, but Ace and the Joes intercept.  (I cannot readily identify the jets they're flying. Sometimes they look like the X-14 Skystriker, only in green, and at other times they look like a green Rockwell B1 Lancer fighter jet.  The Rattlers are sometimes colored green, too.  Nel Yomtov clearly does not know his Joe vehicles.)  Nearby, G.B. Blackrock is enjoying sunbathing on a cruise ship with a lady friend when the overhead battle garners the attention of the ship's passengers.  Blackrock is blissfully unconcerned.  Now, this really is out of character for him.  Given the trouble he's had with Decepticons harrassing him in the past, it would be a far more natural assumption that the Decepticons were targeting his cruise ship for some reason.  (Also, his lady friend is wearing the skimpiest bikini imaginable.  We haven't seen this level of fanservice since the earliest days of the TRANSFORMERS comic, but it's back in force, it seems.)

Serpentor takes advantage of the situation (Cobra Commander is out of the picture by this point), ordering the Joes to stand down or else he'll order the Rattler pilots to destroy the cruise ship and everyone aboard.  As before, Senator Larkin instructs Hawk to simply destroy Power Station Alpha and be done with it.  This time, Hawk actually stands his ground instead of deferring to her.  He points out that millions of taxpayer dollars went into its construction, so he's got an obligation to preserve it.  Besides, the power station's resultant destruction would shower hot shrapnel all over the cruise ship.  The Joes agree to withdraw, but Serpentor has the Rattlers fire on the cruise ship anyway.

The Joes mount a rescue effort, loading the passengers aboard the Killer W.H.A.L.E. hovercrafts.  When a couple of the Joes are still muttering about crazy, shapeshifting robots, Blackrock overhears their conversation and, given his experience with the Autobots, is able to help them out a bit.

Dirge and Bombshell introduce themselves to Cobra.  They can't allow Cobra to take control of Power Station Alpha.  Mindbender wants to find a way to manipulate them as he had done with the power station, so under the pretense of friendship, he offers to forge an alliance.  Dirge can't make this decision for himself, and retreats to consult with Shockwave about the matter.

Mrs. Duranti takes her son to a medical facility where they discover the cerebro-shell implanted inside his brain.  An exploratory operation is the only way to extract it and hopefully return him to normal, but it's a risky move.  It's clear they might kill the kid in the attempt.  Well, like they say, you can't make an omelet without breaking a few legs.  

Mindbender has planted a monitoring device on Dirge, and listen in after he returns to base.  Shockwave aims to use Power Station Alpha to cause massive disturbances along the planet's natural geo-thermal fault lines, intending to harvest the energy of the planet's molten core to revitalize Cybertron.  Mindbender grimly listen in as he realizes the Decepticons will demolish the entire planet.