Up in the air at Seven Island, the psychic barrier ball created by Mewtwo continues to advance towards the Trainer Tower, knocking out any Unown that tries to cut in its way. Inside the transparent globe, Red, Green and Blue gasp at the power and speed the barrier ball demonstrates, and realize just how strong the genetic Pokémon is.

Unable to fight Mewtwo's barrier ball, the Unowns decide to adopt a different strategy and start gathering themselves around the Trainer Tower. They begin spinning around in high speed, and soon engulfs the building like a dark tornado, completely shutting out Mewtwo's barrier ball from it. The genetic Pokémon sends its psychic globe colliding into the tornado, but it only manages to knock off a few Unowns, and the space would swiftly get filled by the others again.

Mewtwo grunts that the rapid acceleration of the symbol Pokémon has generated a powerful field of force despite of their small mass, and this tight network created would pretty much be impregnable to anything. Red wonders what they should do now, and Mewtwo tells him not to worry, reminding him that it has promised to take out all foes of any kind and in any number. Warning the three young trainers to watch their stance, Mewtwo disintegrates the top half of the barrier ball, and begins spinning its psychic spoon and turns it into a swirl of powerful air currents. The currents gradually take the form of a tornado as well, and instantly start sucking off Unowns from their own tornado.

One by one, the Unowns are pulled towards Mewtwo's tornado, and faint as they are spinned ruthlessly amid the psychic swirls. Mewtwo grins that no defense mechanisms stand a chance against this attack, and Red recognizes it as the powerful psywave, a signature move of the genetic Pokémon which gave him equal trouble that many years ago in front of the Cerulean Dungeon.

Slowly, the Unown's own tornado gets completely disrupted as the whole swarm of symbol Pokémon are swept up by the psywave, and Mewtwo brings the attack to an abrupt halt, throwing all the black creatures into the waters below. Still stunned by what they have just seen, Red, Green and Blue gasp that Mewtwo's power alone equals the combined forces of the three elemental ultimate attacks, and the genetic Pokémon grins that it is simply playing by the time limit rule of the Trainer Tower.

With all obstacles cleared ahead of them, Mewtwo brings the three young trainers onto the triangular roof top of the Trainer Tower which has three glass domes at the corners and a big opening at the center. Green comments that traditionally, trainers challenge their skills by competing against time while climbing the building through a series of battles, and Blue says they will, however, start from the top this time.

Red proposes following the theme of the facility, and keeping their battle time with the enemy as short as possible, but then he realizes that Green and Blue are not responding, and turns around to find the two staring at two of the glass domes with astonished looks on their faces. He quickly looks around and discovers that a battered Prof. Oak is in one of the domes, while Blue's parents are in another, all three of them locked up in chains.

Green and Blue gap their mouths wide in bewilderment at the sight of their loved ones, and without much thinking, dash towards the two glass domes. Suddenly, Prof. Oak and Blue's parents disintegrate in particles, and Red and Mewtwo realize with a start that they are simply 3D visual projections. They hurriedly try to stop Green and Blue, but it is too late. The two glass domes open up, and each shoots out a metal arm extensor to clamp around the waists of the two young trainers. Red yells in shock, but another extensor coming from the third glass dome lurks up on him from behind, and grabs him before he notices.

Just when Red, Green and Blue are about to get pulled into the openings of the three separate domes, Mewtwo calmly elongates his psychic spoon in both directions and twirls it around, instantly splitting apart all three metal arm extensors. It then beckons the young trainers to follow, and the four of them swiftly enter the building through the central big opening.

Once they land, everyone looks around and find themselves on a corridor with multiple doors on the side. Red makes sure that his companions are alright, and curses Team Rocket for taking advantage of Green and Blue's sentiment for their families. But Mewtwo reminds him that they are currently in a battle, and it is silly to expect any degree of morality from the enemy. Understanding what Mewtwo is trying to say, Red tells Green and Blue that it is crucial to stick together as the enemy must have somehow seen how strong their combined ultimate attacks could be, and are most likely scheming to separate the three of them.

Mewtwo then says they should save time instead of doing unnecessary searching, and starts using its psychic powers to locate the source of the 3D visual projections earlier. Within seconds, it detects a presence, and points its spoon to one of the doors. The three young trainers quickly break into the room, and Green hollers in shock when he sees his battered grandfather, Oak, chained up against the wall inside a glass column controlled by high-tech machines. The boy frantically runs forward, but Red holds him back and tells him to stay calm and alert to hidden traps.

Green reaches for his Pokéballs to send out his full team of six, and orders Scizor to break the glass with its pincers. However, to his astonishement, the metal bug gets bounced back once it makes contact, and a mechanical voice chuckles that all Pokémon attacks are useful against its restraint system. Red and Green look around and wonder who it is, and a virtual eye suddenly snaps open on a dark liquid crystal sphere right above the glass column trapping Prof. Oak.

The eye speaks in an eerie tone, and calls itself 'r', the mother computer of the Trainer Tower, which is essentially the building itself. Red gasps that the tower possesses a mind on its own, and Green finds it silly that their enemy is a machine. 'r' is ticked off by this remark, however, and unlocks a full row of electric guns, throwing out high voltage currents on Green and his Pokémon.

Mewtwo charges up itself and throws an energy blast at the glass column around Prof. Oak, but it too, barely does any damage, and 'r' chuckles that not even Mewtwo's attacks can harm it. It then sends out a whole bundle of metal arm extensors, each equipped with either drills or spinning blades at the end, and brags that the weapons it possesses are even deadlier than any Pokémon attacks. The drills and blades swiftly plunge towards the young trainers, but Mewtwo builds up its psychic barrier ball again, and manages to hold back the assaults temporarily.

'r' laughs that Green has absolutely no chance in rescuing his grandfather, but the boy has doubts about it and challenges this statement. 'r' points out that its complex system enables it to take every single factor into account, and accurately calculate the outcome in every situation, which is why it is certain that the probability of Green succeeding in saving Prof. Oak is no more than 0%. Putting on a grin, Green remarks that with the capability it claims to have, 'r' must know what his sixth Pokémon is, and the computer assures him that it does. But then, 'r' notices that something is wrong, and only then detects a foreign presence in its network, which is nearing its central system at an extremely high speed, and is no other than the virtual Pokémon, Porygon2.

'r' begins to freak about the unexpected system invasion, and Green remarks that he has used the speed-boosting held item, the Salac Berry, on Porygon2, and thus raised its speed to an unusually high level. Porygon2 soon arrives at the central core of 'r', and Green commands it to unleash a zapcannon, which instantly shuts down the mother computer of the Trainer Tower.

Taking over the restraint system, Porygon2 releases the chains around Prof. Oak's wrists, and disables the glass column that traps him. Red, Green and Blue quickly dash forward to tend to the professor, who assures everyone that he is alright, and tells them to go rescue Blue's parents instead. Green quickly orders a recycle from Porygon2 to reuse the Salac Berry to further boost its speed, and has it shut down the restraint system on Blue's father and mother as well.

Mewtwo scans the rooms with its psychic powers again, and soon locates where the two are held captive. Everyone rushes to the room it pinpoints, and Blue, upon seeing her parents, bursts into tears and throws herself into their arms. The three hug each other tightly as tears of joy roll down their cheeks, and Red, Green and Prof. Oak all put on smiles of relief at the sight of the long-awaited parent-child reunion.

Suddenly, Green senses presence behind them, and alerts everyone to watch out. He turns around to see a whole gang of dull purple creatures edging close towards them, and remarks that it is perhaps still too early to let down their guards…

Thanks To Coronis For Writing this for us