During her time at the G.A.C.C. in space, things have been really hard for Lilo. Like back home, she is bullied by other students, and make fun of her whenever she fails at something. Being human, she is at risk of getting severely hurt and Stitch becomes overprotective of her. It is because of this that she is considered weak to her other classmates, and believe that Lilo’s dependency on Stitch will only slow them down and cause serious problems if they were ever on a real mission.
At first, Lilo was devastated that even in space no one seems to accept her and begins to believe that she will never become anything but a failure. Gantu, Reuben, Jumba, and Stitch try their best to keep her hopes up and remind her of all the rescues she has done in the past in hopes of making her realize how amazing she really is. But despite the support, it only makes Lilo doubt herself more, remembering that usually Stitch was the one who rescued and capture the cousins, while she only named and searched for homes they could belong.
Soon, sadness turns to anger, and now all she wanted to do was prove that she can be just as strong as everyone else. She begins to work harder on her studies and training, and whenever Stitch wants to help her she would reject his assistance. Worried, Stitch turns to the Council Woman and Jumba hoping that they can help Lilo. But instead, they believed that it would be better if Stitch let Lilo work things on her own, after all she’s not a little girl anymore who needed protection 24/7, the best thing to do was give her some space. Even if Stitch was against the idea, he reluctantly agrees and decides to avoid Lilo for a little while.
A few days later, while Stitch had been visiting Jumba, Lilo is asked to give an envelope to Stitch when he returned, in which gives instructions of a new mission Stitch is assigned to. It was then that Lilo decided that this could be her chance to prove how good she can be, and hope that succeeding this can finally make everyone else realize that she didn’t need any protection and wasn’t so weak as everyone believed. She decides to take the risk, and before Stitch would find out, she takes the keys to his Red ship and flies away, not realizing she left the envelope in their room.
Meanwhile, without anyone noticing a prisoner named Zardex escapes from his cell room and is seeking revenge on Stitch for capturing him and his gang. He is considered one of the most dangerous ring leaders in the Galaxy. He has been in jail for 3 years, and during those years he began to grow a dark hatred towards Stitch. His one big goal was to kill him, and has attempted many times to escape in order to go through that dream. Now free, he plans to search for him, and attack at the right moment. Once that’s done, he will set all prisoners free, and attack at the unsuspecting Galactic students.
During his escape in the vents, he overhears the advisor informing a young student about Stitch’s new mission. This was the perfect opportunity, and quickly goes in search for a ship. Once he sees Stitch’s red ship take off, he follows close behind and begins shooting it. Since his attack wasn’t expected, he had successfully damage part of Stitch’s ship, causing it to crash to a close by planet. Witnessing the crash, Zardex is convinced that Stitch didn’t survive it, and turns back to continue his next part of the plan, unaware that the one who he believed was Stitch driving the ship, was in fact Lilo, the young human student he saw earlier.
Few hours later, as Stitch was exiting Jumba’s lab he saw many galactic students screaming and running in fear, confused Stitch tries his best to stop some to ask what’s going on. Many of them told him of the prisoners escaping their cells and attacking them. Fearing for Lilo’s safety, Stitch searched and fought his way back to their dormitories in hope of finding her there, but the only thing there was an envelope of a mission assigned to him, and also his keys were missing. Thinking Lilo is waiting for him at the Ship, he hurries to where the ships are located, but before reaching the room, he is attacked by a group of prisoners. Outnumbered, Stitch is easily beaten and handcuffed. He is then taken to their ring leader, Zardex, who is shocked to see that Stitch was alive, He angrily asks how he escaped his death in the crash earlier. Confused Stitch angrily tells him that he has no clue what he is talking about, and demands to know where Lilo was. Realizing that he was speaking of the human, he informs him that he doesn’t have a clue where she is located, that last time he saw her she was at an office, being told about his mission, and after that he quickly went off and followed a red ship, in which he took down.
It was at that moment that Stitch felt the fur behind his back stood, realizing that Lilo must have been the one who was driving his ship the time it was attacked. Nobody but her knew where he hid his keys, she knew about the mission he was assigned, knowing how much she's been wanting to prove herself to others, it would make sense if she'd plan to take his place and go to his ship. As Stitch put the pieces together, it was then that he began to realize that Lilo…was dead.
His best friend, sister, heroine that he loved with all his heart is gone forever, all because he wasn’t there to protect her, like he promised. The anguish he felt of the horrible news was too much for him, and was soon replaced with the thought of vengeance. His destructive program takes over him and begins attacking everyone who got in his way. Before he could even reach his target, Zardex orders every prisoner to attack Stitch. Despite being very strong and dangerous, he was no match against the large group of aliens who were beating him. The last thing they heard before Stitch went unconscious was a whisper of his friend's name, Lilo.
While this was going on, Nobody noticed a small blue ship that was approaching the school. Lilo was alive, and was driving back to school to warn everyone about a mysterious attacker that needs to be caught. When she was attacked, she quickly when out back and escaped on a small emergency ship that had been installed by Jumba not long ago, luckily she was able to escape on time before it crashed. But now that she’s back, she knows automatically that something is not right. and she sneaks around the halls she finds all her classmates locked away in the cells, and the prisoners who were there earlier were missing. As she searches around, she finds Stitch in one of the cells beaten badly, worried and not wanting to leave him she takes him with her and goes off to look for Jumba. She soon realizes that he’s been captured, and that now the prisoners are planning on attacking the Counsel woman. With Stitch unconscious, and all her friends locked away, it is up to Lilo to find a way to save the day.